Coevolving Pfam domain and position pairs using the CTMP model. Remove the single-copy protein domains if their topology on the gene tree mismatched the toplogy of the species tree at kingdom level. Sorted by the module likelihood score over all the coevolving positions within each domain pair. The first line of each module contains the following information: 1) Coupling mark. * -- two domains co-occur in the same proteins in more than half members. # -- two domains share the same (bottom-level) GO annotation in more than half members. $ -- two domains are likely to be physically or functionally coupled. 2) Module index. 3) Pfam accession number of the first domain. 4) Pfam accession number of the second domain. 5) The number of overlapped species between the two domains. 6) The number of coevolving positions. 7) Module likelihood score. Each line of coevolving positions contains the following information: 1) Index of coevolving position pair. 2) Position 1 (in Pfam's alignment). 3) Position 2 (in Pfam's alignment). 4) Coevolving log odd score. 5) The number of pdb structures where both domains are co-crystalized. 6) The average distance between coevolving amino acids over the available pdb structures. 7) The minimum distance between coevolving amino acids over the available pdb structures. 8) The number of available pdb structures where the coevolving amino acids are less than 10 angstroms. *0 PF00091 PF03953 1329 98 1990.778081 family 1, PF00091: Tubulin/FtsZ family, GTPase domain Structure of the alphabeta tubulin dimer by electron family 2, PF03953: Tubulin/FtsZ family, C-terminal domain Structure of the alphabeta tubulin dimer by electron index pos1 pos2 score npdbs avgdist mindist nshort 0 310 6 101.092550 6 12.1648 11.7076 0 1 324 5 86.153299 6 24.7892 22.2521 0 2 324 6 54.508229 6 25.4655 25.0220 0 3 324 8 32.660225 6 22.0478 21.3796 0 4 324 21 94.888672 6 18.8980 17.8824 0 5 325 5 27.143312 6 21.6687 19.0384 0 6 325 6 12.939194 6 22.2041 21.6042 0 7 325 21 36.820672 6 15.2886 14.3899 0 8 326 4 13.799403 6 18.2825 16.8789 0 9 326 5 74.469866 6 22.2358 19.6004 0 10 326 6 46.919869 6 23.0156 22.4068 0 11 326 8 24.348055 6 19.9206 19.2448 0 12 326 21 82.329649 6 15.6108 14.8527 0 13 329 5 79.571043 6 17.5126 15.1388 0 14 329 6 53.329378 6 18.6093 17.2929 0 15 329 8 27.574869 6 15.6162 13.9319 0 16 329 21 87.494210 6 13.5123 13.0819 0 17 332 5 73.581241 6 15.4924 12.7518 0 18 332 6 42.897360 6 17.3130 16.6688 0 19 332 8 22.319840 6 15.0275 13.2750 0 20 340 5 93.043274 6 13.6861 8.7092 1 21 340 6 58.542776 6 15.3240 13.8423 0 22 340 8 35.323929 6 13.4186 11.4774 0 23 397 4 25.513082 6 5.4771 3.9285 6 24 397 5 112.132405 6 9.0851 7.2531 4 25 397 6 81.408311 6 9.5689 7.1607 4 26 397 8 60.926480 6 6.1370 4.0697 5 27 397 21 122.466215 6 9.8443 7.2338 2 28 399 5 59.727930 6 13.5844 11.5974 0 29 399 6 32.473206 6 13.2299 10.5581 0 30 399 8 16.969137 6 8.8758 6.4041 4 31 399 21 67.742531 6 7.5468 6.7846 6 32 406 4 38.160438 6 27.5918 18.0418 0 33 406 5 116.978370 6 31.5078 22.2615 0 34 406 6 84.314707 6 30.6865 24.8286 0 35 406 8 59.941691 6 26.8812 24.6667 0 36 406 9 93.939451 6 27.6984 17.1634 0 37 406 16 18.606701 6 22.9779 20.2003 0 38 406 21 124.007955 6 17.0627 15.5873 0 39 411 5 10.482062 6 33.9062 21.1857 0 40 411 11 9.141811 6 30.6617 24.8135 0 41 411 16 11.014293 6 25.9716 24.7388 0 42 414 4 23.408654 6 28.8911 19.8375 0 43 414 5 107.874186 6 33.1274 24.6948 0 44 414 6 76.397297 6 32.7677 26.8941 0 45 414 8 57.796919 6 28.9606 25.6563 0 46 414 9 82.260870 6 28.9599 17.9115 0 47 414 21 119.258733 6 19.5151 17.4281 0 48 415 5 72.380588 6 35.7437 27.7358 0 49 415 6 41.454636 6 35.3421 29.8775 0 50 415 8 19.472729 6 32.0342 28.5610 0 51 415 9 48.196453 6 31.0354 20.5079 0 52 415 21 81.056627 6 21.6697 19.8817 0 53 418 16 10.531414 6 22.5838 21.8913 0 54 421 0 11.239577 6 39.2997 37.3164 0 55 421 5 12.470861 6 32.5929 29.3512 0 56 421 11 21.373956 6 27.4675 26.3989 0 57 421 14 17.520790 6 24.8827 23.6108 0 58 421 16 21.162063 6 20.0569 19.1917 0 59 421 21 14.927178 6 17.5596 16.6935 0 60 421 26 9.595712 6 27.3628 26.5971 0 61 422 14 11.624449 6 23.7502 22.0156 0 62 428 6 52.032958 6 26.9918 25.6776 0 63 430 5 29.593483 6 24.1864 20.6115 0 64 430 6 14.903152 6 23.8676 21.9272 0 65 430 21 40.350072 6 12.3954 10.9406 0 66 447 11 15.190459 6 19.1864 17.6559 0 67 447 14 12.713227 6 19.1264 18.4358 0 68 447 16 13.724429 6 15.4441 12.5913 0 69 452 11 12.604195 6 26.8411 25.9472 0 70 455 11 15.410816 6 26.7900 20.9792 0 71 455 14 11.592455 6 28.7477 24.8693 0 72 461 20 14.633740 6 23.7596 21.0818 0 73 461 27 15.125307 6 14.0171 8.3158 2 74 462 5 120.070341 6 33.3652 12.3179 0 75 462 6 83.813518 6 32.3314 14.8167 0 76 462 8 57.758884 6 28.5156 15.5644 0 77 462 9 95.725395 6 30.5602 8.5666 1 78 462 10 57.050306 6 32.9209 15.0494 0 79 462 15 53.973774 6 31.2741 20.4891 0 80 462 25 40.655057 6 16.5228 13.3092 0 81 463 8 13.232779 6 27.6861 17.1828 0 82 463 9 40.796152 6 29.5150 9.0103 1 83 513 5 18.248269 6 26.7910 21.7624 0 84 513 11 12.429010 6 24.5101 20.6666 0 85 513 14 9.464865 6 25.8650 23.2824 0 86 513 16 10.890003 6 22.5431 17.9555 0 87 537 5 47.601347 6 20.3771 18.9551 0 88 537 6 21.212797 6 19.5906 18.6832 0 89 537 9 25.474494 6 18.1877 17.3071 0 90 537 21 55.819407 6 11.1147 10.2860 0 91 553 5 76.673466 6 14.7937 13.4674 0 92 553 6 50.351968 6 14.4440 13.2306 0 93 553 8 29.713023 6 9.2320 7.6014 5 94 553 9 54.464972 6 13.4698 12.1487 0 95 553 21 87.616036 6 11.3301 10.4621 0 96 561 16 12.416586 6 19.6833 17.8585 0 97 562 14 16.321838 6 21.8793 20.7499 0 *1 PF00330 PF00694 206 455 1433.852386 family 1, PF00330: Aconitase family (aconitate hydratase) family 2, PF00694: Aconitase C-terminal domain Steric and conformational features of the aconitase index pos1 pos2 score npdbs avgdist mindist nshort 0 91 57 19.049214 1 10.3422 10.3422 0 1 91 58 22.021917 1 7.8172 7.8172 1 2 91 67 32.158345 1 8.6698 8.6698 1 3 91 261 10.028216 1 10.0356 10.0356 0 4 91 291 13.646666 1 12.9331 12.9331 0 5 93 67 14.405760 1 9.9673 9.9673 1 6 93 69 12.317649 1 14.8431 14.8431 0 7 93 282 12.499709 1 18.2675 18.2675 0 8 94 49 15.987876 1 11.7230 11.7230 0 9 94 57 23.304881 1 10.4432 10.4432 0 10 94 58 22.641463 1 8.0612 8.0612 1 11 94 59 19.814573 1 4.6507 4.6507 1 12 94 62 19.586731 1 5.9638 5.9638 1 13 94 67 35.054561 1 5.9258 5.9258 1 14 94 69 27.081237 1 11.7716 11.7716 0 15 94 70 17.898298 1 10.9095 10.9095 0 16 94 72 19.007523 1 12.8889 12.8889 0 17 94 84 26.131301 1 19.0690 19.0690 0 18 94 260 19.507376 1 8.3598 8.3598 1 19 94 261 9.684491 1 12.3742 12.3742 0 20 94 282 26.119574 1 19.5009 19.5009 0 21 94 283 11.075062 1 16.9707 16.9707 0 22 94 291 13.823892 1 11.2106 11.2106 0 23 95 49 23.575398 1 13.4825 13.4825 0 24 95 57 29.349803 1 13.4499 13.4499 0 25 95 58 32.236156 1 9.6563 9.6563 1 26 95 59 27.714377 1 9.2929 9.2929 1 27 95 62 27.051596 1 9.6657 9.6657 1 28 95 67 43.443582 1 4.4994 4.4994 1 29 95 69 36.229107 1 7.0863 7.0863 1 30 95 70 25.176645 1 8.6485 8.6485 1 31 95 72 29.420269 1 8.5521 8.5521 1 32 95 84 32.970944 1 15.1917 15.1917 0 33 95 260 29.946663 1 3.5533 3.5533 1 34 95 261 17.862711 1 7.9959 7.9959 1 35 95 283 17.021376 1 13.2867 13.2867 0 36 95 291 23.555894 1 7.0093 7.0093 1 37 103 59 12.877479 1 10.8213 10.8213 0 38 103 260 12.443538 1 8.3120 8.3120 1 39 108 41 11.489629 1 15.3951 15.3951 0 40 108 57 10.257015 1 19.1510 19.1510 0 41 108 58 17.049610 1 15.1510 15.1510 0 42 108 59 15.658889 1 14.5310 14.5310 0 43 108 67 23.075708 1 10.5146 10.5146 0 44 108 69 22.363928 1 12.3558 12.3558 0 45 108 72 15.677579 1 12.9335 12.9335 0 46 108 257 18.762860 1 7.3164 7.3164 1 47 108 260 15.093412 1 4.7165 4.7165 1 48 108 264 13.645688 1 11.5551 11.5551 0 49 108 282 20.503662 1 13.0009 13.0009 0 50 108 291 9.191634 1 3.6680 3.6680 1 51 111 19 10.341394 1 30.9068 30.9068 0 52 111 57 16.361325 1 21.3870 21.3870 0 53 111 58 23.406554 1 18.3994 18.3994 0 54 111 59 21.833115 1 16.0763 16.0763 0 55 111 72 21.114921 1 18.6422 18.6422 0 56 111 260 20.827929 1 12.5569 12.5569 0 57 111 261 9.893566 1 17.5958 17.5958 0 58 111 282 27.065042 1 21.4249 21.4249 0 59 111 291 15.201846 1 12.4669 12.4669 0 60 117 13 25.618489 1 30.8555 30.8555 0 61 117 58 29.937508 1 24.9511 24.9511 0 62 117 59 26.193396 1 23.2872 23.2872 0 63 117 69 34.824407 1 20.0631 20.0631 0 64 117 72 26.391760 1 22.1891 22.1891 0 65 117 90 16.367242 1 34.6951 34.6951 0 66 117 257 29.703295 1 18.3968 18.3968 0 67 117 260 26.863080 1 15.3860 15.3860 0 68 117 277 13.722948 1 27.6279 27.6279 0 69 130 58 18.209773 1 25.8709 25.8709 0 70 149 58 12.481494 1 16.1878 16.1878 0 71 150 57 16.784969 1 16.6185 16.6185 0 72 150 58 21.318977 1 14.8631 14.8631 0 73 150 62 14.302122 1 13.4233 13.4233 0 74 150 67 29.972289 1 15.8293 15.8293 0 75 150 70 15.162956 1 20.4686 20.4686 0 76 150 84 20.747292 1 24.5766 24.5766 0 77 150 261 9.912026 1 18.6884 18.6884 0 78 150 291 15.508387 1 19.5851 19.5851 0 79 160 19 10.290533 1 26.2196 26.2196 0 80 160 41 17.297926 1 16.5580 16.5580 0 81 160 49 12.187978 1 8.8102 8.8102 1 82 160 57 16.764411 1 7.8610 7.8610 1 83 160 58 24.191544 1 7.0197 7.0197 1 84 160 59 22.491613 1 3.6967 3.6967 1 85 160 67 28.904005 1 10.6965 10.6965 0 86 160 69 29.741598 1 15.8177 15.8177 0 87 160 70 14.911430 1 13.3563 13.3563 0 88 160 71 9.893003 1 9.5505 9.5505 1 89 160 72 22.139322 1 14.7726 14.7726 0 90 160 78 11.290390 1 16.0311 16.0311 0 91 160 90 11.026413 1 21.7240 21.7240 0 92 160 260 20.749162 1 15.2444 15.2444 0 93 160 261 10.444581 1 13.6109 13.6109 0 94 160 264 19.100640 1 19.3149 19.3149 0 95 160 282 28.395534 1 23.4583 23.4583 0 96 160 291 14.498900 1 19.4509 19.4509 0 97 212 58 12.396482 1 12.9611 12.9611 0 98 388 282 12.096587 1 33.9087 33.9087 0 99 416 257 10.135760 1 18.2103 18.2103 0 100 416 282 13.258390 1 31.5378 31.5378 0 101 451 13 21.745679 1 34.5413 34.5413 0 102 451 19 13.451587 1 28.7876 28.7876 0 103 451 41 19.106487 1 19.7158 19.7158 0 104 451 49 15.485608 1 14.0692 14.0692 0 105 451 57 16.789179 1 10.8839 10.8839 0 106 451 58 25.674239 1 9.7731 9.7731 1 107 451 59 22.124443 1 6.4943 6.4943 1 108 451 62 16.454362 1 5.4381 5.4381 1 109 451 67 31.797508 1 8.1083 8.1083 1 110 451 69 30.757460 1 13.7342 13.7342 0 111 451 70 17.446385 1 11.2152 11.2152 0 112 451 71 13.506697 1 11.3699 11.3699 0 113 451 72 23.729287 1 14.8233 14.8233 0 114 451 90 13.554300 1 25.6677 25.6677 0 115 451 199 13.522488 1 26.4128 26.4128 0 116 451 260 22.292107 1 14.7862 14.7862 0 117 451 261 13.283688 1 15.2916 15.2916 0 118 451 264 21.073581 1 17.6878 17.6878 0 119 451 282 27.322932 1 25.3316 25.3316 0 120 451 291 17.676378 1 18.6382 18.6382 0 121 492 260 28.526425 1 19.6051 19.6051 0 122 497 59 11.452296 1 19.2210 19.2210 0 123 497 260 12.248629 1 16.9637 16.9637 0 124 510 59 17.350178 1 14.0095 14.0095 0 125 510 67 28.739426 1 21.2619 21.2619 0 126 510 70 11.251845 1 24.6980 24.6980 0 127 510 72 17.751294 1 26.4179 26.4179 0 128 510 257 20.911928 1 20.0250 20.0250 0 129 510 260 17.833754 1 24.7220 24.7220 0 130 528 19 12.512745 1 33.6381 33.6381 0 131 528 58 25.515811 1 21.9460 21.9460 0 132 528 59 24.092330 1 17.4582 17.4582 0 133 528 67 30.509935 1 23.0483 23.0483 0 134 528 69 30.923019 1 27.5982 27.5982 0 135 528 72 22.659075 1 26.8394 26.8394 0 136 528 260 23.052628 1 20.8314 20.8314 0 137 528 264 21.692734 1 28.7492 28.7492 0 138 528 282 29.753359 1 21.7280 21.7280 0 139 528 291 17.099369 1 21.1990 21.1990 0 140 540 257 21.960433 1 29.7651 29.7651 0 141 596 49 12.519694 1 17.8326 17.8326 0 142 596 67 31.408037 1 24.7865 24.7865 0 143 596 260 17.517503 1 20.0598 20.0598 0 144 597 49 26.194415 1 18.8855 18.8855 0 145 597 57 33.204713 1 23.6530 23.6530 0 146 597 58 25.927623 1 23.4999 23.4999 0 147 597 59 24.727934 1 18.6663 18.6663 0 148 597 62 28.745289 1 23.7264 23.7264 0 149 597 67 46.713909 1 26.7722 26.7722 0 150 597 69 31.045367 1 30.5394 30.5394 0 151 597 70 29.014493 1 29.7139 29.7139 0 152 597 72 23.287474 1 28.5921 28.5921 0 153 597 84 36.182284 1 27.0831 27.0831 0 154 597 90 16.176750 1 27.6465 27.6465 0 155 597 257 26.208922 1 20.0636 20.0636 0 156 597 260 24.589176 1 23.2323 23.2323 0 157 597 261 14.582280 1 24.3376 24.3376 0 158 597 282 29.484050 1 19.3488 19.3488 0 159 597 291 19.638944 1 23.1764 23.1764 0 160 599 257 9.475166 1 23.7198 23.7198 0 161 603 58 12.257628 1 30.4041 30.4041 0 162 603 69 18.609142 1 35.1996 35.1996 0 163 605 57 9.309343 1 26.6935 26.6935 0 164 605 58 12.152305 1 25.0719 25.0719 0 165 605 257 12.720759 1 19.0211 19.0211 0 166 606 19 26.857078 1 27.7742 27.7742 0 167 606 49 42.023366 1 18.9767 18.9767 0 168 606 57 46.997509 1 24.5976 24.5976 0 169 606 58 41.271490 1 22.0555 22.0555 0 170 606 62 45.920803 1 22.8747 22.8747 0 171 606 67 61.126030 1 22.6364 22.6364 0 172 606 69 46.392559 1 25.5798 25.5798 0 173 606 72 37.491614 1 24.4750 24.4750 0 174 606 84 50.701831 1 23.7349 23.7349 0 175 606 260 38.297990 1 17.1369 17.1369 0 176 606 261 25.603077 1 20.4011 20.4011 0 177 606 264 36.304418 1 24.2622 24.2622 0 178 606 282 43.003957 1 12.4730 12.4730 0 179 606 283 35.781954 1 9.3002 9.3002 1 180 606 291 32.513390 1 15.8125 15.8125 0 181 624 57 11.205230 1 21.2607 21.2607 0 182 624 58 14.327794 1 17.2905 17.2905 0 183 624 67 23.261748 1 14.4774 14.4774 0 184 624 84 15.676342 1 19.4569 19.4569 0 185 624 260 11.973500 1 7.3145 7.3145 1 186 629 41 13.147987 1 20.2415 20.2415 0 187 629 58 18.097799 1 19.1711 19.1711 0 188 629 59 17.080255 1 17.7088 17.7088 0 189 629 72 15.898888 1 18.1845 18.1845 0 190 629 260 16.245154 1 10.0530 10.0530 0 191 629 282 22.618588 1 15.0387 15.0387 0 192 629 291 11.522760 1 8.3272 8.3272 1 193 630 57 10.299243 1 26.8810 26.8810 0 194 630 58 12.449468 1 23.0035 23.0035 0 195 630 59 12.743529 1 21.6156 21.6156 0 196 630 67 25.091213 1 19.2945 19.2945 0 197 630 72 11.423897 1 21.6595 21.6595 0 198 630 260 11.821364 1 12.9161 12.9161 0 199 630 291 9.014124 1 9.6034 9.6034 1 200 635 13 15.570534 1 31.3254 31.3254 0 201 635 58 16.787399 1 25.6162 25.6162 0 202 635 69 24.031856 1 23.6639 23.6639 0 203 635 257 17.126000 1 18.0086 18.0086 0 204 670 13 11.316548 1 40.7581 40.7581 0 205 670 58 13.538417 1 24.1704 24.1704 0 206 670 69 18.858811 1 34.1581 34.1581 0 207 670 72 11.790115 1 30.9630 30.9630 0 208 670 257 15.711690 1 24.9808 24.9808 0 209 670 260 11.741928 1 29.3518 29.3518 0 210 695 58 11.060849 1 26.8240 26.8240 0 211 695 69 15.163220 1 34.9968 34.9968 0 212 695 72 9.303728 1 31.4383 31.4383 0 213 695 257 12.580160 1 25.1058 25.1058 0 214 695 260 10.037260 1 27.8996 27.8996 0 215 695 282 13.320278 1 20.7608 20.7608 0 216 701 13 21.390109 1 30.1409 30.1409 0 217 701 19 11.309589 1 23.5429 23.5429 0 218 701 41 19.330830 1 17.3701 17.3701 0 219 701 49 11.454218 1 21.6328 21.6328 0 220 701 57 16.171817 1 26.9785 26.9785 0 221 701 58 23.001715 1 26.4399 26.4399 0 222 701 59 20.765505 1 24.7799 24.7799 0 223 701 62 15.123674 1 29.9040 29.9040 0 224 701 67 29.615521 1 32.0722 32.0722 0 225 701 69 28.822505 1 33.3677 33.3677 0 226 701 70 13.460700 1 31.8848 31.8848 0 227 701 71 9.562305 1 27.2088 27.2088 0 228 701 72 19.713474 1 29.3322 29.3322 0 229 701 90 12.355896 1 20.1125 20.1125 0 230 701 257 25.220769 1 23.1855 23.1855 0 231 701 260 21.429770 1 25.0803 25.0803 0 232 701 261 10.891918 1 25.3258 25.3258 0 233 701 282 25.426566 1 16.6276 16.6276 0 234 701 291 15.683993 1 25.9916 25.9916 0 235 735 13 14.315392 1 29.3765 29.3765 0 236 735 41 12.096364 1 17.7914 17.7914 0 237 735 58 17.063545 1 27.9450 27.9450 0 238 735 59 15.648709 1 25.2794 25.2794 0 239 735 69 22.243698 1 32.6010 32.6010 0 240 735 257 18.498014 1 21.6043 21.6043 0 241 735 260 15.404354 1 23.2321 23.2321 0 242 735 282 19.808801 1 12.5008 12.5008 0 243 735 291 10.713510 1 22.4792 22.4792 0 244 742 13 10.507851 1 24.4542 24.4542 0 245 742 58 13.430752 1 26.0688 26.0688 0 246 742 59 13.088846 1 24.2474 24.2474 0 247 742 257 13.576128 1 19.0883 19.0883 0 248 742 282 19.537820 1 7.9616 7.9616 1 249 758 41 11.493290 1 22.1613 22.1613 0 250 758 57 11.751071 1 32.1719 32.1719 0 251 758 58 16.825191 1 30.7138 30.7138 0 252 758 62 10.235604 1 31.9855 31.9855 0 253 758 67 25.526878 1 32.2452 32.2452 0 254 758 72 14.503476 1 32.3974 32.3974 0 255 758 260 14.416519 1 25.2072 25.2072 0 256 758 282 20.053561 1 14.8541 14.8541 0 257 803 13 10.345512 1 29.6301 29.6301 0 258 803 58 13.686348 1 20.8832 20.8832 0 259 803 59 11.338715 1 16.8944 16.8944 0 260 803 67 19.274673 1 25.0458 25.0458 0 261 803 69 18.457114 1 27.4608 27.4608 0 262 803 72 11.307944 1 24.6253 24.6253 0 263 803 84 10.870314 1 19.1812 19.1812 0 264 803 257 14.333173 1 16.8557 16.8557 0 265 803 260 11.526528 1 19.8194 19.8194 0 266 803 264 10.054570 1 25.6802 25.6802 0 267 803 282 18.113618 1 12.8824 12.8824 0 268 843 265 11.809656 1 43.6652 43.6652 0 269 1201 57 30.283617 1 16.1118 16.1118 0 270 1201 67 44.667782 1 26.5338 26.5338 0 271 1201 70 28.055182 1 24.3208 24.3208 0 272 1201 260 31.852410 1 22.9756 22.9756 0 273 1202 57 18.035762 1 19.4850 19.4850 0 274 1202 261 9.317835 1 21.8143 21.8143 0 275 1902 260 21.287790 1 38.6991 38.6991 0 276 1907 58 10.438131 1 22.5533 22.5533 0 277 1907 67 14.504293 1 31.8581 31.8581 0 278 1907 69 14.412284 1 34.3065 34.3065 0 279 1907 282 13.718745 1 32.9092 32.9092 0 280 1908 57 13.865862 1 14.9418 14.9418 0 281 1908 58 20.766755 1 17.6744 17.6744 0 282 1908 59 17.747759 1 14.3881 14.3881 0 283 1908 62 11.256444 1 19.1609 19.1609 0 284 1908 69 25.119093 1 29.4721 29.4721 0 285 1908 260 17.667021 1 28.5262 28.5262 0 286 1908 282 25.012929 1 29.4252 29.4252 0 287 1908 291 13.677275 1 31.8300 31.8300 0 288 1910 13 15.750027 1 42.1734 42.1734 0 289 1910 41 13.091405 1 23.1456 23.1456 0 290 1910 57 12.134235 1 18.7911 18.7911 0 291 1910 58 19.627127 1 20.6165 20.6165 0 292 1910 62 10.646059 1 20.9114 20.9114 0 293 1910 69 23.601675 1 31.1956 31.1956 0 294 1910 72 16.851715 1 28.5409 28.5409 0 295 1910 257 20.841411 1 22.5733 22.5733 0 296 1910 260 17.551612 1 27.3174 27.3174 0 297 1916 58 9.808270 1 22.6365 22.6365 0 298 1916 67 15.193736 1 27.7555 27.7555 0 299 1916 69 14.065481 1 32.2628 32.2628 0 300 1916 257 10.638453 1 23.1013 23.1013 0 301 1916 282 14.288752 1 27.5989 27.5989 0 302 1918 19 12.844315 1 41.9848 41.9848 0 303 1918 41 18.450313 1 32.7607 32.7607 0 304 1918 49 14.613601 1 25.5643 25.5643 0 305 1918 57 18.670794 1 28.1803 28.1803 0 306 1918 58 26.583945 1 29.5290 29.5290 0 307 1918 59 23.142962 1 23.7663 23.7663 0 308 1918 62 17.008607 1 28.9311 28.9311 0 309 1918 67 31.042384 1 34.3092 34.3092 0 310 1918 69 30.850829 1 39.0703 39.0703 0 311 1918 70 16.283732 1 37.1034 37.1034 0 312 1918 71 10.145285 1 31.6841 31.6841 0 313 1918 72 24.119796 1 37.1315 37.1315 0 314 1918 90 12.377536 1 36.4326 36.4326 0 315 1918 199 10.775217 1 46.4982 46.4982 0 316 1918 257 28.468626 1 29.8751 29.8751 0 317 1918 260 23.502460 1 34.2074 34.2074 0 318 1918 261 11.737449 1 33.7692 33.7692 0 319 1918 264 22.524903 1 41.1202 41.1202 0 320 1918 277 10.999316 1 30.4771 30.4771 0 321 1918 282 28.116778 1 33.7187 33.7187 0 322 1918 291 16.607037 1 35.7799 35.7799 0 323 1919 13 18.328058 1 51.2001 51.2001 0 324 1919 41 16.151763 1 33.6647 33.6647 0 325 1919 58 22.609678 1 31.7088 31.7088 0 326 1919 59 19.933307 1 25.9760 25.9760 0 327 1919 69 26.796820 1 41.3650 41.3650 0 328 1919 72 18.193610 1 39.2324 39.2324 0 329 1919 257 21.155831 1 32.0211 32.0211 0 330 1919 260 19.377079 1 36.3306 36.3306 0 331 1921 57 15.787212 1 23.5691 23.5691 0 332 1921 58 12.985622 1 25.5419 25.5419 0 333 1921 62 12.488642 1 25.3272 25.3272 0 334 1921 67 27.754620 1 31.7747 31.7747 0 335 1921 69 17.909776 1 36.2299 36.2299 0 336 1921 70 11.514885 1 33.6423 33.6423 0 337 1931 13 18.685299 1 60.0954 60.0954 0 338 1931 57 14.730758 1 34.1419 34.1419 0 339 1931 58 20.674822 1 36.6737 36.6737 0 340 1931 69 26.284666 1 48.3224 48.3224 0 341 1931 257 19.895949 1 40.9636 40.9636 0 342 1960 59 15.407400 1 16.1136 16.1136 0 343 1971 257 24.240311 1 27.4938 27.4938 0 344 1971 260 21.377313 1 31.9408 31.9408 0 345 1971 291 17.646058 1 33.9127 33.9127 0 346 1975 13 26.190210 1 55.6902 55.6902 0 347 1975 19 15.341200 1 47.0549 47.0549 0 348 1975 41 22.787812 1 37.6793 37.6793 0 349 1975 49 17.143975 1 29.1677 29.1677 0 350 1975 57 20.104795 1 30.2474 30.2474 0 351 1975 58 29.767572 1 31.5257 31.5257 0 352 1975 59 24.388375 1 25.9531 25.9531 0 353 1975 62 20.516618 1 30.0780 30.0780 0 354 1975 67 34.141091 1 35.4827 35.4827 0 355 1975 69 34.482732 1 40.8646 40.8646 0 356 1975 70 19.079573 1 38.8106 38.8106 0 357 1975 71 12.380272 1 34.1375 34.1375 0 358 1975 72 25.828802 1 39.6626 39.6626 0 359 1975 78 16.446075 1 40.7279 40.7279 0 360 1975 84 27.560886 1 41.1614 41.1614 0 361 1975 90 16.508190 1 41.4556 41.4556 0 362 1975 199 14.709354 1 49.9115 49.9115 0 363 1975 257 28.651363 1 32.6235 32.6235 0 364 1975 260 26.991245 1 37.2249 37.2249 0 365 1975 261 14.933227 1 37.1009 37.1009 0 366 1975 264 23.582949 1 43.9928 43.9928 0 367 1975 277 13.802164 1 36.8801 36.8801 0 368 1975 282 30.284601 1 39.2361 39.2361 0 369 1975 283 10.553334 1 37.9494 37.9494 0 370 1975 291 22.019528 1 39.2045 39.2045 0 371 1976 58 11.257980 1 28.6438 28.6438 0 372 2006 58 14.722730 1 31.2934 31.2934 0 373 2009 19 12.651923 1 40.1491 40.1491 0 374 2009 58 26.520199 1 26.0045 26.0045 0 375 2009 90 14.089122 1 34.2457 34.2457 0 376 2009 260 23.802370 1 37.2687 37.2687 0 377 2009 261 12.030192 1 33.8593 33.8593 0 378 2009 282 28.879607 1 39.5121 39.5121 0 379 2035 57 19.144718 1 17.2883 17.2883 0 380 2035 58 26.867166 1 18.0977 18.0977 0 381 2035 261 12.282486 1 23.9189 23.9189 0 382 2039 13 15.093560 1 36.8344 36.8344 0 383 2039 41 12.738693 1 16.6640 16.6640 0 384 2039 57 10.191122 1 9.8870 9.8870 1 385 2039 58 19.106579 1 12.2407 12.2407 0 386 2039 59 16.286455 1 8.9905 8.9905 1 387 2039 62 9.348360 1 13.8040 13.8040 0 388 2039 67 24.817609 1 21.3950 21.3950 0 389 2039 69 22.601529 1 23.7858 23.7858 0 390 2039 70 10.052684 1 20.7110 20.7110 0 391 2039 72 16.593598 1 21.2052 21.2052 0 392 2039 84 16.411290 1 19.7444 19.7444 0 393 2039 257 20.569521 1 17.9174 17.9174 0 394 2039 260 16.846452 1 22.7894 22.7894 0 395 2039 264 14.596203 1 26.6917 26.6917 0 396 2039 282 22.261990 1 24.5833 24.5833 0 397 2039 291 10.779288 1 26.2459 26.2459 0 398 2047 19 12.536940 1 24.2997 24.2997 0 399 2047 49 25.081036 1 5.9446 5.9446 1 400 2047 57 29.230192 1 4.6921 4.6921 1 401 2047 58 24.838782 1 6.0277 6.0277 1 402 2047 59 21.031072 1 3.3155 3.3155 1 403 2047 62 25.745670 1 5.6209 5.6209 1 404 2047 67 43.034902 1 13.6954 13.6954 0 405 2047 69 29.597767 1 16.9197 16.9197 0 406 2047 70 27.225817 1 14.0328 14.0328 0 407 2047 72 22.639506 1 15.2810 15.2810 0 408 2047 84 33.168842 1 17.6314 17.6314 0 409 2047 90 11.577688 1 19.0563 19.0563 0 410 2047 257 25.936267 1 12.9212 12.9212 0 411 2047 260 22.493266 1 17.7368 17.7368 0 412 2047 261 11.547939 1 14.0186 14.0186 0 413 2047 264 19.669089 1 20.6001 20.6001 0 414 2047 282 25.487741 1 24.2956 24.2956 0 415 2047 283 16.502355 1 24.8145 24.8145 0 416 2047 291 17.154909 1 22.1000 22.1000 0 417 2048 58 22.941649 1 10.2100 10.2100 0 418 2048 261 13.169740 1 18.7081 18.7081 0 419 2048 291 16.033012 1 27.3228 27.3228 0 420 2077 13 20.295532 1 39.5824 39.5824 0 421 2077 57 14.754347 1 16.2528 16.2528 0 422 2077 58 23.629487 1 18.8715 18.8715 0 423 2077 69 27.368404 1 30.0457 30.0457 0 424 2077 257 22.111225 1 23.3155 23.3155 0 425 2077 260 21.010083 1 27.9101 27.9101 0 426 2077 261 9.938351 1 24.0633 24.0633 0 427 2077 291 15.359200 1 30.4089 30.4089 0 428 2080 13 31.347228 1 37.9913 37.9913 0 429 2080 19 20.834784 1 26.6928 26.6928 0 430 2080 41 28.985030 1 18.4768 18.4768 0 431 2080 49 22.207611 1 12.1092 12.1092 0 432 2080 57 25.171206 1 14.2462 14.2462 0 433 2080 58 34.699770 1 16.4695 16.4695 0 434 2080 59 31.397148 1 12.5966 12.5966 0 435 2080 62 24.982525 1 17.9643 17.9643 0 436 2080 67 40.432529 1 24.9838 24.9838 0 437 2080 69 39.006775 1 27.7200 27.7200 0 438 2080 70 24.454757 1 24.7628 24.7628 0 439 2080 72 31.340370 1 24.8317 24.8317 0 440 2080 84 31.530591 1 22.3117 22.3117 0 441 2080 90 23.211307 1 20.8309 20.8309 0 442 2080 256 11.834707 1 20.1111 20.1111 0 443 2080 257 34.328258 1 20.3333 20.3333 0 444 2080 260 32.529359 1 25.1216 25.1216 0 445 2080 261 22.144692 1 21.5335 21.5335 0 446 2080 264 29.199163 1 29.8507 29.8507 0 447 2080 282 36.099951 1 22.9415 22.9415 0 448 2080 283 15.566038 1 24.4222 24.4222 0 449 2080 291 28.148470 1 27.5565 27.5565 0 450 2085 57 13.160253 1 10.6225 10.6225 0 451 2085 67 26.678342 1 20.5156 20.5156 0 452 2085 70 12.433303 1 18.0939 18.0939 0 453 2085 260 15.428295 1 19.5522 19.5522 0 454 2108 58 11.024461 1 29.5490 29.5490 0 *2 PF01326 PF02896 158 363 1311.129167 family 1, PF01326: Pyruvate phosphate dikinase, PEP/pyruvate binding domain Swiveling-domain mechanism for enzymatic phosphotransfer family 2, PF02896: PEP-utilising enzyme, TIM barrel domain Swiveling-domain mechanism for enzymatic phosphotransfer index pos1 pos2 score npdbs avgdist mindist nshort 0 24 268 12.504506 1 62.1732 62.1732 0 1 24 625 10.717651 1 42.5942 42.5942 0 2 28 268 11.430244 1 61.2408 61.2408 0 3 28 549 15.991308 1 57.6325 57.6325 0 4 32 268 10.502120 1 64.3159 64.3159 0 5 55 268 11.483078 1 65.9208 65.9208 0 6 215 268 16.839947 1 79.1210 79.1210 0 7 215 270 9.150133 1 80.3868 80.3868 0 8 215 271 11.790728 1 84.7623 84.7623 0 9 215 569 12.193200 1 78.7390 78.7390 0 10 228 266 12.622539 1 68.4188 68.4188 0 11 228 268 22.999479 1 66.5835 66.5835 0 12 228 270 14.930023 1 67.6477 67.6477 0 13 228 363 15.267429 1 73.6909 73.6909 0 14 228 380 15.568116 1 72.5409 72.5409 0 15 228 590 10.873665 1 54.9161 54.9161 0 16 228 624 9.460115 1 44.7150 44.7150 0 17 228 625 21.400339 1 46.7485 46.7485 0 18 228 629 18.692067 1 44.4886 44.4886 0 19 229 239 11.160057 1 67.4366 67.4366 0 20 229 266 13.679246 1 66.7855 66.7855 0 21 229 268 24.496849 1 64.7362 64.7362 0 22 229 270 16.264139 1 65.6531 65.6531 0 23 229 271 19.449170 1 70.2042 70.2042 0 24 229 363 16.027267 1 71.4480 71.4480 0 25 229 380 16.522358 1 70.6533 70.6533 0 26 229 557 9.232625 1 58.9104 58.9104 0 27 229 574 10.117899 1 52.6957 52.6957 0 28 229 590 13.054318 1 52.5257 52.5257 0 29 229 624 11.023423 1 42.5506 42.5506 0 30 229 629 20.904546 1 42.2927 42.2927 0 31 229 687 15.167098 1 51.1373 51.1373 0 32 231 549 25.315768 1 57.5896 57.5896 0 33 231 663 18.570814 1 39.2728 39.2728 0 34 236 268 9.667673 1 50.4292 50.4292 0 35 241 268 9.312839 1 50.4292 50.4292 0 36 248 268 10.242696 1 64.6092 64.6092 0 37 320 268 22.147207 1 72.1773 72.1773 0 38 320 270 13.906323 1 72.9703 72.9703 0 39 320 363 14.372775 1 77.9969 77.9969 0 40 320 380 14.900066 1 78.6312 78.6312 0 41 320 590 11.928205 1 59.1849 59.1849 0 42 320 625 21.573281 1 52.9376 52.9376 0 43 320 629 19.733465 1 52.0788 52.0788 0 44 320 687 13.299003 1 62.0005 62.0005 0 45 322 268 14.756444 1 64.6392 64.6392 0 46 322 271 9.273215 1 69.9485 69.9485 0 47 322 625 12.609549 1 46.1886 46.1886 0 48 322 629 11.229805 1 46.5613 46.5613 0 49 323 363 10.891716 1 75.5182 75.5182 0 50 323 380 11.915702 1 75.9878 75.9878 0 51 323 629 16.515158 1 48.6593 48.6593 0 52 380 266 11.238071 1 68.0157 68.0157 0 53 380 268 21.826237 1 64.1407 64.1407 0 54 380 270 13.762590 1 64.8176 64.8176 0 55 380 363 14.055194 1 69.0070 69.0070 0 56 380 380 14.642901 1 70.8866 70.8866 0 57 380 441 9.748286 1 64.2732 64.2732 0 58 380 571 11.405589 1 67.2591 67.2591 0 59 380 590 11.958863 1 51.2340 51.2340 0 60 380 625 20.352663 1 47.0088 47.0088 0 61 380 629 19.729750 1 48.5311 48.5311 0 62 380 664 9.903030 1 51.6930 51.6930 0 63 380 687 13.328697 1 58.9133 58.9133 0 64 427 629 21.042546 1 47.7981 47.7981 0 65 447 268 16.746083 1 76.5048 76.5048 0 66 447 363 9.207462 1 81.3314 81.3314 0 67 447 380 10.197796 1 82.7955 82.7955 0 68 447 625 16.784984 1 57.3129 57.3129 0 69 447 629 14.499964 1 56.1812 56.1812 0 70 466 268 19.351817 1 76.7684 76.7684 0 71 466 270 11.042152 1 77.3062 77.3062 0 72 466 363 12.170862 1 82.2115 82.2115 0 73 466 380 12.395844 1 82.7201 82.7201 0 74 466 409 10.889716 1 86.3973 86.3973 0 75 466 571 11.564337 1 74.0729 74.0729 0 76 466 625 17.024142 1 56.6161 56.6161 0 77 466 629 14.764746 1 53.9569 53.9569 0 78 476 266 9.826262 1 74.9279 74.9279 0 79 476 268 19.423985 1 72.6681 72.6681 0 80 476 270 11.275118 1 73.3504 73.3504 0 81 476 271 13.943764 1 77.9535 77.9535 0 82 476 363 10.855395 1 78.7072 78.7072 0 83 476 380 12.407097 1 78.3272 78.3272 0 84 476 625 17.513723 1 52.3514 52.3514 0 85 476 629 14.697069 1 49.3240 49.3240 0 86 476 687 9.846141 1 59.7091 59.7091 0 87 477 663 9.179975 1 52.5637 52.5637 0 88 480 268 18.616824 1 67.6506 67.6506 0 89 480 270 9.956305 1 68.2707 68.2707 0 90 480 363 10.718326 1 73.6554 73.6554 0 91 480 380 12.340729 1 72.9546 72.9546 0 92 480 629 15.608795 1 43.7127 43.7127 0 93 480 687 9.880557 1 54.5314 54.5314 0 94 483 268 12.383435 1 64.1105 64.1105 0 95 483 625 11.768279 1 43.5703 43.5703 0 96 483 629 9.913406 1 39.7900 39.7900 0 97 484 239 13.059580 1 67.4424 67.4424 0 98 484 266 16.372829 1 64.7225 64.7225 0 99 484 268 27.738743 1 62.7257 62.7257 0 100 484 270 19.211733 1 63.2419 63.2419 0 101 484 271 21.767456 1 67.9212 67.9212 0 102 484 272 10.113702 1 67.0072 67.0072 0 103 484 363 17.224847 1 68.6054 68.6054 0 104 484 380 20.477302 1 67.5399 67.5399 0 105 484 552 14.256308 1 52.2839 52.2839 0 106 484 556 15.104684 1 54.1167 54.1167 0 107 484 557 11.762593 1 54.6120 54.6120 0 108 484 565 11.509018 1 58.7253 58.7253 0 109 484 574 11.128738 1 49.8097 49.8097 0 110 484 590 14.005863 1 49.6678 49.6678 0 111 484 597 10.921004 1 48.9514 48.9514 0 112 484 624 13.218104 1 39.7562 39.7562 0 113 484 625 25.735929 1 42.1530 42.1530 0 114 484 629 21.897563 1 38.0167 38.0167 0 115 484 690 28.959274 1 47.9202 47.9202 0 116 485 239 9.293021 1 68.9123 68.9123 0 117 485 268 22.649517 1 63.5494 63.5494 0 118 485 270 14.349092 1 63.9171 63.9171 0 119 485 363 14.107416 1 69.0930 69.0930 0 120 485 380 14.831402 1 67.9040 67.9040 0 121 485 409 12.865316 1 72.5558 72.5558 0 122 485 571 11.925755 1 58.1094 58.1094 0 123 485 590 11.239921 1 50.1991 50.1991 0 124 485 625 20.478554 1 42.9595 42.9595 0 125 485 629 19.170109 1 38.1594 38.1594 0 126 485 664 9.735883 1 46.1938 46.1938 0 127 485 687 13.054146 1 50.4027 50.4027 0 128 492 239 9.616104 1 58.4938 58.4938 0 129 492 251 11.043017 1 52.0509 52.0509 0 130 492 266 12.483618 1 54.8332 54.8332 0 131 492 268 22.861752 1 52.3214 52.3214 0 132 492 270 15.048595 1 52.5849 52.5849 0 133 492 271 18.636203 1 57.2590 57.2590 0 134 492 363 15.250545 1 57.4838 57.4838 0 135 492 380 15.708688 1 57.3156 57.3156 0 136 492 409 12.668226 1 63.6207 63.6207 0 137 492 552 10.445252 1 43.0023 43.0023 0 138 492 556 10.201977 1 44.4234 44.4234 0 139 492 571 12.794495 1 49.5990 49.5990 0 140 492 574 9.480234 1 41.0587 41.0587 0 141 492 590 12.639524 1 38.4779 38.4779 0 142 492 624 9.877926 1 29.3087 29.3087 0 143 492 625 21.704956 1 31.8230 31.8230 0 144 492 628 10.469359 1 28.8998 28.8998 0 145 492 629 20.556427 1 28.1150 28.1150 0 146 492 664 11.108564 1 36.9969 36.9969 0 147 492 687 14.635189 1 42.0078 42.0078 0 148 493 266 10.814387 1 54.8867 54.8867 0 149 493 268 19.972616 1 52.7847 52.7847 0 150 493 270 12.106404 1 53.0473 53.0473 0 151 493 271 14.639182 1 57.7536 57.7536 0 152 493 363 11.881598 1 58.1297 58.1297 0 153 493 380 13.694097 1 57.1241 57.1241 0 154 493 571 11.203376 1 48.4116 48.4116 0 155 493 625 16.463367 1 32.2273 32.2273 0 156 493 629 15.540637 1 27.4435 27.4435 0 157 493 664 9.507917 1 36.6944 36.6944 0 158 493 687 11.265978 1 41.0650 41.0650 0 159 497 266 18.171339 1 51.2198 51.2198 0 160 497 268 30.383775 1 49.4676 49.4676 0 161 497 270 21.432895 1 49.7752 49.7752 0 162 497 271 24.396429 1 54.4855 54.4855 0 163 497 272 12.659584 1 54.0438 54.0438 0 164 497 363 20.795289 1 54.9441 54.9441 0 165 497 378 17.717273 1 48.6306 48.6306 0 166 497 380 21.717132 1 53.0027 53.0027 0 167 497 552 17.025160 1 37.7398 37.7398 0 168 497 556 17.049439 1 38.5030 38.5030 0 169 497 557 14.115690 1 39.1266 39.1266 0 170 497 574 14.581437 1 35.4202 35.4202 0 171 497 590 17.651168 1 36.1840 36.1840 0 172 497 597 13.419648 1 36.5573 36.5573 0 173 497 624 15.411750 1 26.7557 26.7557 0 174 497 625 27.553558 1 29.2486 29.2486 0 175 497 629 25.658273 1 23.2049 23.2049 0 176 497 664 17.039770 1 33.4684 33.4684 0 177 497 665 9.512180 1 31.9993 31.9993 0 178 508 268 19.777282 1 49.5053 49.5053 0 179 508 270 11.941390 1 50.2205 50.2205 0 180 508 271 14.399681 1 54.8978 54.8978 0 181 508 378 10.089875 1 48.5287 48.5287 0 182 508 625 18.699645 1 29.6770 29.6770 0 183 520 266 10.453024 1 61.1465 61.1465 0 184 520 268 17.530507 1 59.7557 59.7557 0 185 520 270 9.951884 1 60.5810 60.5810 0 186 520 271 11.971204 1 65.2489 65.2489 0 187 520 380 12.564548 1 63.8531 63.8531 0 188 520 625 16.179469 1 39.6479 39.6479 0 189 520 690 20.756445 1 44.0293 44.0293 0 190 524 268 12.663494 1 62.7161 62.7161 0 191 524 271 9.003540 1 68.4546 68.4546 0 192 524 625 13.294449 1 42.9908 42.9908 0 193 524 629 9.851549 1 39.8516 39.8516 0 194 526 266 12.745932 1 66.4659 66.4659 0 195 526 268 18.947247 1 64.9557 64.9557 0 196 526 270 11.567975 1 66.3364 66.3364 0 197 526 363 12.232939 1 72.8228 72.8228 0 198 526 380 13.010454 1 71.0239 71.0239 0 199 526 590 9.988578 1 54.4658 54.4658 0 200 526 629 17.520525 1 43.7956 43.7956 0 201 530 268 21.847969 1 71.0784 71.0784 0 202 530 270 14.002592 1 72.5570 72.5570 0 203 530 363 14.087504 1 78.5891 78.5891 0 204 530 380 14.273185 1 77.7416 77.7416 0 205 530 590 12.067123 1 60.1954 60.1954 0 206 530 629 19.890398 1 52.0488 52.0488 0 207 531 268 17.974879 1 70.5371 70.5371 0 208 531 270 11.299662 1 72.0940 72.0940 0 209 531 271 12.831821 1 76.2212 76.2212 0 210 531 552 9.135301 1 63.8091 63.8091 0 211 531 629 12.840972 1 52.5867 52.5867 0 212 532 268 13.700980 1 71.3048 71.3048 0 213 532 271 9.766451 1 76.8302 76.8302 0 214 532 625 12.967534 1 53.2419 53.2419 0 215 532 629 11.019270 1 53.7605 53.7605 0 216 534 268 18.252583 1 75.3289 75.3289 0 217 534 270 10.055583 1 77.0376 77.0376 0 218 534 363 10.134018 1 83.3589 83.3589 0 219 534 380 11.344229 1 82.2329 82.2329 0 220 534 629 14.758329 1 58.8383 58.8383 0 221 537 268 17.193972 1 72.2061 72.2061 0 222 537 270 9.321839 1 74.0035 74.0035 0 223 537 363 9.677322 1 80.5165 80.5165 0 224 537 380 10.882176 1 79.0699 79.0699 0 225 537 625 15.947814 1 54.7318 54.7318 0 226 537 629 14.760670 1 55.4583 55.4583 0 227 539 268 28.607813 1 65.0697 65.0697 0 228 539 270 20.395666 1 66.8947 66.8947 0 229 539 271 23.647675 1 70.8616 70.8616 0 230 539 272 11.805950 1 69.8172 69.8172 0 231 539 378 17.522821 1 69.4223 69.4223 0 232 539 550 16.579205 1 62.2423 62.2423 0 233 539 552 15.715591 1 59.0066 59.0066 0 234 539 557 12.424753 1 64.1895 64.1895 0 235 539 565 12.527097 1 66.7718 66.7718 0 236 539 574 13.930105 1 54.8844 54.8844 0 237 539 590 16.222242 1 55.9133 55.9133 0 238 539 597 12.163124 1 55.2006 55.2006 0 239 539 625 26.889171 1 47.6779 47.6779 0 240 540 268 31.515397 1 61.6693 61.6693 0 241 540 270 23.914397 1 63.5871 63.5871 0 242 540 271 26.300304 1 67.5532 67.5532 0 243 540 272 14.648543 1 66.6277 66.6277 0 244 540 557 16.246620 1 60.4085 60.4085 0 245 540 565 16.943855 1 62.8529 62.8529 0 246 540 597 15.929650 1 52.7685 52.7685 0 247 540 625 30.368819 1 44.2882 44.2882 0 248 543 239 20.707551 1 50.3592 50.3592 0 249 543 266 21.083999 1 54.9025 54.9025 0 250 543 268 32.833679 1 53.3022 53.3022 0 251 543 270 25.475208 1 55.4396 55.4396 0 252 543 271 28.141798 1 59.3399 59.3399 0 253 543 272 17.452752 1 58.5976 58.5976 0 254 543 363 24.565689 1 62.3796 62.3796 0 255 543 379 13.957108 1 57.0041 57.0041 0 256 543 380 25.246222 1 60.2315 60.2315 0 257 543 400 15.237252 1 60.7087 60.7087 0 258 543 401 9.646674 1 55.6529 55.6529 0 259 543 408 14.226431 1 55.6304 55.6304 0 260 543 409 22.050916 1 55.5414 55.5414 0 261 543 441 17.612893 1 53.1704 53.1704 0 262 543 556 20.259044 1 53.5703 53.5703 0 263 543 557 17.754518 1 52.7524 52.7524 0 264 543 564 16.956036 1 55.3482 55.3482 0 265 543 571 21.152629 1 49.0573 49.0573 0 266 543 574 18.958365 1 42.9257 42.9257 0 267 543 576 9.694922 1 40.2222 40.2222 0 268 543 590 22.231442 1 45.8440 45.8440 0 269 543 597 18.579909 1 45.6909 45.6909 0 270 543 624 18.552134 1 36.5403 36.5403 0 271 543 625 30.440025 1 36.5719 36.5719 0 272 543 629 29.761871 1 37.8296 37.8296 0 273 543 662 9.816896 1 34.3255 34.3255 0 274 543 664 21.574543 1 33.5747 33.5747 0 275 543 665 14.302854 1 29.8651 29.8651 0 276 543 685 12.757071 1 39.7003 39.7003 0 277 543 687 23.647091 1 38.9352 38.9352 0 278 543 691 12.334600 1 33.4693 33.4693 0 279 580 268 16.661116 1 57.5138 57.5138 0 280 580 380 10.116707 1 64.6080 64.6080 0 281 580 625 13.852412 1 41.5830 41.5830 0 282 580 629 11.238016 1 43.7993 43.7993 0 283 584 239 15.495869 1 68.8591 68.8591 0 284 584 266 22.854914 1 73.2620 73.2620 0 285 584 268 30.940368 1 71.0458 71.0458 0 286 584 270 22.435506 1 72.7116 72.7116 0 287 584 271 25.013097 1 76.6134 76.6134 0 288 584 272 12.695457 1 75.1079 75.1079 0 289 584 363 19.858197 1 78.8422 78.8422 0 290 584 380 24.765558 1 78.0129 78.0129 0 291 584 557 15.883244 1 71.0872 71.0872 0 292 584 590 16.046308 1 61.5847 61.5847 0 293 584 597 13.854772 1 60.6175 60.6175 0 294 584 624 18.554116 1 53.0131 53.0131 0 295 584 625 29.075449 1 53.8067 53.8067 0 296 584 629 23.882894 1 55.0939 55.0939 0 297 584 665 11.084348 1 48.9922 48.9922 0 298 588 268 34.169514 1 65.2113 65.2113 0 299 588 270 25.232720 1 66.7087 66.7087 0 300 588 272 15.652940 1 69.3015 69.3015 0 301 588 276 34.615963 1 68.1350 68.1350 0 302 655 363 13.630198 1 82.1793 82.1793 0 303 655 590 10.869570 1 66.1624 66.1624 0 304 668 268 11.532573 1 57.3008 57.3008 0 305 668 625 10.751373 1 40.8350 40.8350 0 306 682 363 15.652967 1 59.5390 59.5390 0 307 682 380 16.539189 1 56.5544 56.5544 0 308 682 574 9.335941 1 38.6739 38.6739 0 309 682 590 12.081469 1 43.6672 43.6672 0 310 682 624 10.510520 1 34.0335 34.0335 0 311 682 629 19.538728 1 34.5237 34.5237 0 312 700 266 12.498927 1 54.3962 54.3962 0 313 700 270 10.037440 1 55.8633 55.8633 0 314 700 571 13.278894 1 45.9824 45.9824 0 315 700 624 9.750119 1 36.3008 36.3008 0 316 704 239 9.286872 1 60.2122 60.2122 0 317 704 266 10.951926 1 64.4290 64.4290 0 318 704 268 20.609422 1 62.8195 62.8195 0 319 704 270 13.789853 1 64.7274 64.7274 0 320 704 271 17.662002 1 68.8122 68.8122 0 321 704 363 14.043743 1 71.5218 71.5218 0 322 704 380 13.259100 1 69.5678 69.5678 0 323 704 556 9.379701 1 61.1398 61.1398 0 324 704 571 10.743450 1 58.0489 58.0489 0 325 704 574 9.080766 1 51.6086 51.6086 0 326 704 590 12.472129 1 54.1389 54.1389 0 327 704 625 19.338810 1 45.0432 45.0432 0 328 704 629 19.594129 1 45.2031 45.2031 0 329 704 664 10.769207 1 42.6425 42.6425 0 330 704 687 15.214431 1 47.7777 47.7777 0 331 705 268 14.240047 1 66.4388 66.4388 0 332 705 276 15.612678 1 69.6162 69.6162 0 333 705 625 11.877633 1 48.4274 48.4274 0 334 705 629 9.969289 1 48.4674 48.4674 0 335 727 268 20.139593 1 47.9147 47.9147 0 336 727 270 12.373060 1 50.2456 50.2456 0 337 727 271 14.563698 1 54.2547 54.2547 0 338 727 363 11.444726 1 57.5352 57.5352 0 339 727 378 9.530636 1 51.3124 51.3124 0 340 727 380 12.351048 1 54.6639 54.6639 0 341 727 409 9.962383 1 50.1946 50.1946 0 342 727 569 14.160989 1 47.5709 47.5709 0 343 727 571 9.229373 1 42.3099 42.3099 0 344 727 625 18.640331 1 31.0347 31.0347 0 345 727 629 15.640228 1 31.3548 31.3548 0 346 727 687 11.170865 1 32.0430 32.0430 0 347 728 268 13.788058 1 43.2547 43.2547 0 348 728 271 9.037214 1 49.4630 49.4630 0 349 728 625 12.494390 1 25.4895 25.4895 0 350 728 629 11.220480 1 25.4088 25.4088 0 351 736 266 12.393824 1 44.5182 44.5182 0 352 736 268 20.157429 1 43.0036 43.0036 0 353 736 270 12.676840 1 45.3435 45.3435 0 354 736 271 15.847265 1 49.2193 49.2193 0 355 736 378 15.192700 1 47.1515 47.1515 0 356 736 380 14.565358 1 49.9282 49.9282 0 357 736 441 12.197392 1 42.8663 42.8663 0 358 736 552 9.864319 1 37.2075 37.2075 0 359 736 556 9.449779 1 43.7949 43.7949 0 360 736 590 9.031624 1 36.6959 36.6959 0 361 736 625 18.242084 1 26.8450 26.8450 0 362 736 629 16.304115 1 28.5274 28.5274 0 *3 PF00391 PF01326 166 80 825.127904 family 1, PF00391: PEP-utilising enzyme, mobile domain Swiveling-domain mechanism for enzymatic phosphotransfer family 2, PF01326: Pyruvate phosphate dikinase, PEP/pyruvate binding domain Swiveling-domain mechanism for enzymatic phosphotransfer index pos1 pos2 score npdbs avgdist mindist nshort 0 53 322 11.482950 1 20.2038 20.2038 0 1 53 493 17.864482 1 33.0228 33.0228 0 2 53 532 9.494372 1 25.9407 25.9407 0 3 53 537 13.249667 1 27.5336 27.5336 0 4 53 728 10.393210 1 21.2406 21.2406 0 5 55 466 23.377008 1 32.7515 32.7515 0 6 55 485 29.395063 1 33.5579 33.5579 0 7 55 492 29.236314 1 24.7806 24.7806 0 8 55 543 42.643130 1 16.5937 16.5937 0 9 55 727 27.400456 1 21.9087 21.9087 0 10 55 728 19.420126 1 19.4729 19.4729 0 11 58 526 13.499837 1 25.7268 25.7268 0 12 61 24 41.018608 1 34.1254 34.1254 0 13 61 28 31.714546 1 32.1605 32.1605 0 14 61 32 34.449870 1 35.6074 35.6074 0 15 61 228 55.178473 1 28.2787 28.2787 0 16 61 229 57.344762 1 27.3528 27.3528 0 17 61 248 37.963784 1 23.0542 23.0542 0 18 61 320 56.116644 1 27.7986 27.7986 0 19 61 322 45.366747 1 19.2143 19.2143 0 20 61 323 52.232760 1 25.8866 25.8866 0 21 61 332 33.574281 1 28.5952 28.5952 0 22 61 380 56.524228 1 16.8433 16.8433 0 23 61 447 49.932488 1 32.5904 32.5904 0 24 61 466 47.866509 1 36.1052 36.1052 0 25 61 476 50.467213 1 34.2035 34.2035 0 26 61 480 51.042549 1 31.9331 31.9331 0 27 61 483 41.886661 1 30.3561 30.3561 0 28 61 484 58.564470 1 30.2209 30.2209 0 29 61 485 55.494299 1 32.8388 32.8388 0 30 61 492 57.564593 1 21.6905 21.6905 0 31 61 493 48.804855 1 26.6310 26.6310 0 32 61 497 63.265790 1 28.7555 28.7555 0 33 61 520 49.641376 1 34.3731 34.3731 0 34 61 524 43.184479 1 30.7229 30.7229 0 35 61 526 51.772071 1 29.2667 29.2667 0 36 61 530 56.014096 1 28.2092 28.2092 0 37 61 531 47.572244 1 27.6112 27.6112 0 38 61 532 44.817204 1 26.0281 26.0281 0 39 61 534 48.947509 1 31.1822 31.1822 0 40 61 537 49.499590 1 29.6166 29.6166 0 41 61 539 59.699587 1 23.1887 23.1887 0 42 61 540 61.501416 1 23.1860 23.1860 0 43 61 543 70.564038 1 19.6374 19.6374 0 44 61 580 42.728002 1 18.4200 18.4200 0 45 61 655 54.635599 1 36.5999 36.5999 0 46 61 668 42.018194 1 31.2134 31.2134 0 47 61 704 56.713711 1 25.7745 25.7745 0 48 61 705 42.190172 1 26.5513 26.5513 0 49 61 727 52.245403 1 21.5720 21.5720 0 50 61 728 44.965922 1 18.6843 18.6843 0 51 61 736 54.124795 1 18.7510 18.7510 0 52 73 543 14.778912 1 19.3241 19.3241 0 53 86 484 10.697964 1 29.6496 29.6496 0 54 86 497 13.972652 1 31.6661 31.6661 0 55 86 543 17.624736 1 7.4656 7.4656 1 56 86 584 13.669709 1 17.6679 17.6679 0 57 107 543 11.090369 1 6.5749 6.5749 1 58 112 228 14.257739 1 27.7956 27.7956 0 59 112 229 14.466973 1 27.8415 27.8415 0 60 112 320 15.165778 1 33.5412 33.5412 0 61 112 323 9.405249 1 31.7600 31.7600 0 62 112 380 14.855162 1 30.0202 30.0202 0 63 112 480 10.821530 1 33.5871 33.5871 0 64 112 492 14.063847 1 26.0831 26.0831 0 65 112 493 12.536140 1 27.7819 27.7819 0 66 112 526 13.553216 1 25.7690 25.7690 0 67 112 530 12.835663 1 28.6626 28.6626 0 68 112 543 26.337044 1 10.8785 10.8785 0 69 112 682 15.620852 1 10.8565 10.8565 0 70 112 704 14.127585 1 20.4404 20.4404 0 71 117 229 14.262222 1 32.3941 32.3941 0 72 117 320 15.032071 1 33.4357 33.4357 0 73 117 380 13.334350 1 27.6385 27.6385 0 74 117 447 9.195572 1 41.3824 41.3824 0 75 117 480 9.980677 1 38.5073 38.5073 0 76 117 492 13.972865 1 31.5347 31.5347 0 77 117 526 15.201770 1 30.3353 30.3353 0 78 117 543 24.618260 1 13.0041 13.0041 0 79 117 704 14.453495 1 21.6305 21.6305 0 *4 PF01228 PF02901 67 112 526.100992 family 1, PF01228: Glycine radical family 2, PF02901: Pyruvate formate lyase Structure and mechanism of the glycyl radical enzyme index pos1 pos2 score npdbs avgdist mindist nshort 0 0 338 10.156790 2 37.6740 36.6019 0 1 0 432 14.521194 2 38.8939 38.8256 0 2 0 652 10.592655 2 18.6600 18.6455 0 3 0 845 9.264771 2 35.8725 31.2947 0 4 0 973 10.412500 2 19.3686 19.3015 0 5 0 1029 9.807042 2 18.8172 18.7458 0 6 2 2 10.568249 2 38.2673 33.6353 0 7 2 973 9.336135 2 23.0766 22.6470 0 8 4 2 10.011029 2 39.7282 37.3123 0 9 4 338 9.373925 2 35.5297 33.2973 0 10 7 124 11.437416 2 30.0860 28.4910 0 11 7 170 10.517845 2 32.6238 29.7265 0 12 7 176 9.701900 2 31.5871 29.5004 0 13 7 178 10.861788 2 35.5059 34.2456 0 14 7 260 12.684838 2 37.9853 36.0906 0 15 7 529 15.756680 2 27.0372 26.9863 0 16 7 552 11.085264 2 33.8127 33.5318 0 17 7 616 17.428910 2 25.7699 24.7476 0 18 7 646 11.938873 2 32.9016 31.9621 0 19 7 648 9.017138 2 25.9166 24.9550 0 20 7 691 11.709067 2 23.7711 22.1810 0 21 7 718 15.879045 1 13.7424 13.7424 0 22 7 819 9.612503 2 31.5848 30.4151 0 23 7 1089 11.121746 2 12.6622 11.4207 0 24 8 55 10.972717 2 33.0792 27.5433 0 25 8 616 12.745270 2 27.8755 26.4444 0 26 8 718 12.120391 1 16.8296 16.8296 0 27 10 55 9.859286 2 39.5204 33.7916 0 28 10 260 10.621703 2 41.6603 39.3584 0 29 10 529 11.846425 2 30.0318 29.7359 0 30 10 616 13.627306 2 28.5805 26.6811 0 31 10 617 9.317875 2 30.4055 27.6337 0 32 10 646 9.043757 2 35.8687 35.2216 0 33 10 691 9.045708 2 27.5829 26.6126 0 34 10 718 12.150344 1 14.4480 14.4480 0 35 26 616 12.377804 2 19.8566 17.4175 0 36 26 718 9.883672 1 26.9759 26.9759 0 37 51 338 10.398183 2 30.9327 27.9690 0 38 51 432 14.099297 2 27.4039 26.9418 0 39 52 2 11.514655 2 34.2659 31.0178 0 40 57 124 13.842454 2 27.9593 25.4398 0 41 57 167 9.628600 2 42.0149 40.3616 0 42 57 170 11.163416 2 33.1588 31.0811 0 43 57 176 10.238694 2 34.4399 33.3244 0 44 57 178 12.106230 2 39.4934 38.9388 0 45 57 260 13.515014 2 29.8044 27.4040 0 46 57 409 9.604844 2 29.9134 29.6088 0 47 57 411 9.133479 2 32.3321 31.5695 0 48 57 529 16.278779 2 17.5768 17.2943 0 49 57 552 11.681885 2 21.4391 20.9918 0 50 57 615 9.955632 2 17.1716 13.0968 0 51 57 616 18.723158 2 19.4504 16.1064 0 52 57 646 13.025780 2 25.1663 24.8760 0 53 57 648 10.913766 2 18.4487 18.0450 0 54 57 691 11.825445 2 22.2259 19.8049 0 55 57 706 11.467784 2 28.5940 28.2786 0 56 57 718 16.559218 1 26.8507 26.8507 0 57 57 790 9.159934 2 27.2998 26.1759 0 58 57 819 9.396578 2 30.9120 29.7988 0 59 57 853 10.077799 2 33.3028 29.2165 0 60 57 885 9.331397 2 14.1364 13.7181 0 61 57 1089 12.146138 2 18.3486 18.2189 0 62 65 2 10.751450 2 36.7851 26.2232 0 63 65 401 9.147653 2 40.6832 39.1546 0 64 65 973 10.497449 2 36.3927 33.8715 0 65 89 6 11.781951 2 30.6533 29.9615 0 66 89 11 16.944034 2 33.1779 31.1636 0 67 89 24 10.103062 2 34.6611 26.7959 0 68 89 28 14.479253 2 34.0679 25.3790 0 69 89 35 10.547327 2 33.9364 16.1554 0 70 89 83 11.971866 2 40.2723 39.3735 0 71 89 97 13.273598 2 39.8559 37.7146 0 72 89 175 10.641582 2 46.2282 46.0477 0 73 89 177 14.660813 2 44.1583 43.1382 0 74 89 249 12.921287 2 27.7447 26.7522 0 75 89 263 12.067734 2 30.1086 28.2772 0 76 89 269 13.699412 2 41.5673 40.9654 0 77 89 325 11.219629 2 42.9621 40.3864 0 78 89 327 9.728974 2 42.6684 40.7470 0 79 89 338 18.152419 2 39.8532 38.8877 0 80 89 341 13.111390 2 43.9614 41.5295 0 81 89 368 10.739319 2 46.8505 45.0668 0 82 89 437 10.004334 2 28.7087 27.8117 0 83 89 523 15.222162 2 29.5331 29.3751 0 84 89 542 9.754508 2 13.6260 12.6979 0 85 89 574 14.845747 2 8.8220 8.1446 2 86 89 575 13.299787 2 3.6017 2.9974 2 87 89 608 9.487404 2 12.8323 8.8831 1 88 89 612 13.471283 2 10.4772 8.3335 1 89 89 619 13.447458 2 17.6977 12.8843 0 90 89 714 9.112488 2 42.5745 41.6168 0 91 89 765 12.275584 2 39.3624 38.1405 0 92 89 788 10.537637 2 37.0760 36.6310 0 93 89 818 9.850827 2 42.3266 42.0498 0 94 89 850 13.941163 2 36.2860 34.4469 0 95 89 897 15.155222 2 28.2699 27.4767 0 96 89 898 9.993533 2 33.4593 33.3687 0 97 89 905 10.431475 2 41.1431 37.5304 0 98 89 973 16.678458 2 36.4013 33.8978 0 99 90 11 11.051916 2 36.5646 35.3198 0 100 90 177 9.945491 2 43.4515 42.3532 0 101 90 269 9.003601 2 45.7649 45.5191 0 102 90 338 13.333871 2 42.1679 40.0566 0 103 90 523 9.809621 2 31.3981 30.9952 0 104 90 897 9.228177 2 24.4975 23.8872 0 105 90 973 10.901667 2 33.1576 30.6276 0 106 127 2 11.569193 2 31.0051 26.8303 0 107 133 616 11.545924 2 32.4476 28.9185 0 108 133 718 9.977445 1 25.5441 25.5441 0 109 138 432 10.989568 2 39.1297 37.9154 0 110 150 616 12.528645 2 24.3657 21.8085 0 111 150 718 9.342421 1 32.0438 32.0438 0 *5 PF01262 PF05222 176 32 453.611614 family 1, PF01262: Alanine dehydrogenase/PNT, C-terminal domain Lysine metabolism in higher plants. family 2, PF05222: Alanine dehydrogenase/PNT, N-terminal domain Lysine metabolism in higher plants. index pos1 pos2 score npdbs avgdist mindist nshort 0 5 174 35.496280 2 29.6512 23.1444 0 1 5 235 43.068264 2 26.2651 17.1486 0 2 5 241 23.150842 2 19.5787 11.2357 0 3 6 235 42.784499 2 25.2926 15.6245 0 4 6 241 26.308746 2 18.5495 9.4855 1 5 8 171 27.344331 1 33.9844 33.9844 0 6 8 238 12.923694 2 25.8726 16.4732 0 7 12 241 14.346027 2 14.5501 4.3559 1 8 13 174 16.119940 2 31.0085 19.1215 0 9 13 235 21.813005 2 20.8102 6.7936 1 10 13 241 9.414644 2 17.0627 6.5594 1 11 14 174 12.509114 2 31.4781 16.4599 0 12 14 235 18.546598 2 21.7295 5.3685 1 13 15 174 22.938563 2 34.5612 19.7584 0 14 15 235 31.977494 2 24.1735 8.5348 1 15 15 241 12.251097 2 19.7040 6.6339 1 16 20 171 24.042140 1 42.1133 42.1133 0 17 20 220 40.950734 2 33.9644 21.2905 0 18 20 238 11.140437 2 27.8869 13.3628 0 19 45 241 10.088215 2 13.9421 13.8321 0 20 65 235 39.105617 2 20.0462 18.5529 0 21 76 235 44.590819 2 21.6750 20.5880 0 22 145 235 18.007441 2 24.9637 24.2539 0 23 152 174 25.767806 2 21.6443 20.9687 0 24 152 235 33.558961 2 18.1998 16.9955 0 25 152 241 16.829708 2 14.8976 14.5936 0 26 153 174 12.121992 2 20.1987 18.4111 0 27 153 235 18.173720 2 14.8970 13.2266 0 28 154 174 12.546208 2 18.7825 18.4437 0 29 154 235 20.075668 2 15.6859 14.7869 0 30 277 238 13.429273 2 19.5949 19.5838 0 31 285 220 16.203656 2 13.2101 10.7131 0 *6 PF00390 PF03949 214 43 423.847286 family 1, PF00390: Malic enzyme, N-terminal domain family 2, PF03949: Malic enzyme, NAD binding domain index pos1 pos2 score npdbs avgdist mindist nshort 0 31 0 22.797970 4 19.8178 18.6058 0 1 31 389 18.382223 4 21.9426 20.7802 0 2 31 390 17.696419 4 23.7924 22.9560 0 3 39 0 24.505261 4 22.9011 21.2260 0 4 39 213 10.555777 4 38.9827 37.1743 0 5 39 389 22.279509 4 22.4165 19.9126 0 6 84 0 19.243252 4 21.0434 20.1987 0 7 160 0 19.638560 4 17.2299 16.6629 0 8 160 284 9.289735 4 19.0482 15.5297 0 9 162 0 25.019534 4 14.1796 13.7544 0 10 162 284 13.217941 4 19.3947 17.4794 0 11 163 0 25.618942 4 16.7879 16.4115 0 12 163 213 10.913982 4 35.3399 33.6809 0 13 163 284 11.718153 4 21.8562 18.8446 0 14 175 0 17.109294 4 18.9698 18.5883 0 15 286 0 35.953805 4 13.2915 12.7367 0 16 286 284 22.517630 4 29.3824 27.3300 0 17 286 375 17.755641 4 25.2126 23.5349 0 18 288 0 12.229999 4 8.4166 7.7943 4 19 289 0 28.176876 4 6.3944 6.0461 4 20 289 213 12.732523 4 28.9439 27.9497 0 21 289 284 13.957826 4 21.9287 20.6418 0 22 289 288 13.995668 4 23.9741 21.8100 0 23 289 375 10.110042 4 21.5506 21.1031 0 24 289 389 22.466679 4 10.4854 10.3080 0 25 294 0 17.628169 4 7.1259 6.1394 4 26 294 389 13.422655 4 15.8399 15.7045 0 27 294 390 11.246055 4 18.6991 18.2346 0 28 299 0 18.678599 4 3.6134 2.9146 4 29 299 389 12.602356 4 16.8853 15.2689 0 30 299 390 12.442028 4 19.9161 19.3890 0 31 303 0 31.990404 4 3.6954 3.4810 4 32 303 1 11.351939 4 3.2701 2.9863 4 33 303 213 14.013348 4 26.0330 25.5776 0 34 303 221 10.486715 4 22.1111 21.7726 0 35 303 389 29.261741 4 12.8384 10.3274 0 36 306 0 30.636183 4 10.4218 9.2918 1 37 306 213 13.832357 4 33.7533 33.3540 0 38 306 284 15.369007 4 30.8611 29.1083 0 39 306 375 11.894518 4 30.8105 29.8056 0 40 306 389 24.390799 4 14.9187 13.9970 0 41 306 390 24.377213 4 17.0970 16.3304 0 42 322 0 10.303917 4 2.8251 2.6144 4 *7 PF00009 PF03764 441 36 423.495557 family 1, PF00009: Elongation factor Tu GTP binding domain Visualization of elongation factor Tu on the Escherichia family 2, PF03764: Elongation factor G, domain IV index pos1 pos2 score npdbs avgdist mindist nshort 0 33 213 15.870509 1 90.6623 90.6623 0 1 66 147 12.288080 1 100.4587 100.4587 0 2 66 213 22.643667 1 102.3200 102.3200 0 3 66 220 9.160688 1 95.9653 95.9653 0 4 93 154 13.319574 1 94.0919 94.0919 0 5 165 154 31.802258 1 72.0782 72.0782 0 6 361 147 15.338973 1 65.8316 65.8316 0 7 361 154 27.348937 1 60.1405 60.1405 0 8 361 213 23.250244 1 69.0621 69.0621 0 9 365 147 28.073266 1 69.3882 69.3882 0 10 365 211 24.329519 1 75.3383 75.3383 0 11 365 213 32.159728 1 73.4147 73.4147 0 12 365 220 19.470117 1 66.8604 66.8604 0 13 451 154 17.412413 1 62.2380 62.2380 0 14 482 147 23.357344 1 72.9837 72.9837 0 15 482 154 39.806392 1 68.0996 68.0996 0 16 482 211 25.958358 1 78.8619 78.8619 0 17 482 213 36.377750 1 76.6122 76.6122 0 18 482 220 20.490232 1 69.9368 69.9368 0 19 493 147 53.668930 1 72.3827 72.3827 0 20 493 154 66.564050 1 67.1065 67.1065 0 21 493 211 53.326530 1 79.2037 79.2037 0 22 493 213 63.787899 1 77.1879 77.1879 0 23 493 220 47.441990 1 70.6706 70.6706 0 24 510 147 28.111516 1 80.3460 80.3460 0 25 510 154 41.457843 1 75.7216 75.7216 0 26 510 211 30.146668 1 86.8181 86.8181 0 27 510 213 39.481876 1 84.4549 84.4549 0 28 510 220 23.713223 1 77.7785 77.7785 0 29 533 154 29.920494 1 84.0197 84.0197 0 30 533 211 20.301475 1 90.6853 90.6853 0 31 883 147 28.633120 1 92.9572 92.9572 0 32 883 154 46.477130 1 87.7446 87.7446 0 33 883 211 31.377699 1 94.4197 94.4197 0 34 883 213 40.327131 1 92.6694 92.6694 0 35 965 213 11.780676 1 91.2475 91.2475 0 *8 PF05681 PF05683 93 35 421.717714 family 1, PF05681: Fumarate hydratase (Fumerase) Oxygen- and growth rate-dependent regulation of Escherichia family 2, PF05683: Fumarase C-terminus Oxygen- and growth rate-dependent regulation of Escherichia index pos1 pos2 score npdbs avgdist mindist nshort 0 19 106 19.327620 0 - - 0 1 19 139 10.170590 0 - - 0 2 121 117 14.662059 0 - - 0 3 121 121 21.112780 0 - - 0 4 121 178 17.203361 0 - - 0 5 121 235 12.284247 0 - - 0 6 132 106 22.820538 0 - - 0 7 132 117 12.932754 0 - - 0 8 201 106 20.493475 0 - - 0 9 253 106 15.014163 0 - - 0 10 285 117 12.301107 0 - - 0 11 298 121 10.704881 0 - - 0 12 300 125 12.355484 0 - - 0 13 300 189 14.894947 0 - - 0 14 300 235 9.662983 0 - - 0 15 304 120 16.674289 0 - - 0 16 307 106 13.312693 0 - - 0 17 309 106 19.609365 0 - - 0 18 322 106 12.029259 0 - - 0 19 327 106 21.294592 0 - - 0 20 377 233 9.583945 0 - - 0 21 377 240 9.419600 0 - - 0 22 385 106 15.779340 0 - - 0 23 399 106 23.244471 0 - - 0 24 399 139 15.487603 0 - - 0 25 412 121 16.343904 0 - - 0 26 422 121 12.312512 0 - - 0 27 422 189 10.926911 0 - - 0 28 422 198 13.886287 0 - - 0 29 423 106 13.423236 0 - - 0 30 425 121 18.239925 0 - - 0 31 425 178 11.723284 0 - - 0 32 425 189 12.965256 0 - - 0 33 427 121 15.456934 0 - - 0 34 435 106 14.070203 0 - - 0 $9 PF00738 PF04941 83 29 346.883297 family 1, PF00738: Polyhedrin family 2, PF04941: Late expression factor 8 (LEF-8) Characterization of late gene expression factors lef-9 and index pos1 pos2 score npdbs avgdist mindist nshort 0 57 626 14.511235 0 - - 0 1 69 626 10.719798 0 - - 0 2 77 626 14.412655 0 - - 0 3 94 626 10.471599 0 - - 0 4 96 626 11.308269 0 - - 0 5 100 626 9.919565 0 - - 0 6 101 626 9.294940 0 - - 0 7 111 626 15.414427 0 - - 0 8 112 626 9.522137 0 - - 0 9 113 626 12.256127 0 - - 0 10 115 626 11.692267 0 - - 0 11 119 626 14.600061 0 - - 0 12 128 626 11.811998 0 - - 0 13 129 626 15.194352 0 - - 0 14 131 626 12.952135 0 - - 0 15 147 626 15.334056 0 - - 0 16 148 626 14.050895 0 - - 0 17 151 626 16.629718 0 - - 0 18 159 626 16.124061 0 - - 0 19 170 626 18.063768 0 - - 0 20 170 648 9.595963 0 - - 0 21 170 730 9.612961 0 - - 0 22 173 626 11.549757 0 - - 0 23 174 626 20.130841 0 - - 0 24 174 648 9.808902 0 - - 0 25 174 730 9.537837 0 - - 0 26 195 626 12.624589 0 - - 0 27 206 626 10.075844 0 - - 0 28 210 626 12.710791 0 - - 0 *10 PF00298 PF03946 292 23 299.768825 family 1, PF00298: Ribosomal protein L11, RNA binding domain High resolution solution structure of ribosomal protein family 2, PF03946: Ribosomal protein L11, N-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 0 19 22.749910 1 16.4314 16.4314 0 1 0 26 9.322093 1 18.2533 18.2533 0 2 0 61 19.417916 1 3.0007 3.0007 1 3 0 69 38.360465 1 20.9472 20.9472 0 4 2 69 22.515312 1 27.3283 27.3283 0 5 3 69 20.136620 1 27.1885 27.1885 0 6 12 19 14.186644 1 24.0995 24.0995 0 7 12 35 12.199776 1 16.8074 16.8074 0 8 12 61 15.191511 1 11.8158 11.8158 0 9 13 69 35.465994 1 27.5351 27.5351 0 10 16 69 23.816259 1 27.1573 27.1573 0 11 45 19 25.489311 1 23.2628 23.2628 0 12 45 31 39.988062 1 27.2872 27.2872 0 13 45 32 20.818494 1 29.3577 29.3577 0 14 47 69 29.884419 1 27.7491 27.7491 0 15 52 35 10.093715 1 30.1453 30.1453 0 16 52 69 33.260661 1 32.1135 32.1135 0 17 89 19 10.689703 1 20.0746 20.0746 0 18 92 26 9.576069 1 23.2841 23.2841 0 19 92 32 26.257955 1 19.5937 19.5937 0 20 120 30 9.817552 1 23.3312 23.3312 0 21 120 61 9.890062 1 14.0469 14.0469 0 22 120 69 26.222775 1 28.2282 28.2282 0 *11 PF00809 PF02965 103 40 287.303050 family 1, PF00809: Pterin binding enzyme Crystal structure of the anti-bacterial sulfonamide drug family 2, PF02965: Vitamin B12 dependent methionine synthase, activation domain The structure of the C-terminal domain of methionine index pos1 pos2 score npdbs avgdist mindist nshort 0 88 27 11.726878 0 - - 0 1 210 27 9.434349 0 - - 0 2 227 6 9.385558 0 - - 0 3 246 27 9.974751 0 - - 0 4 248 27 12.952520 0 - - 0 5 248 103 16.622772 0 - - 0 6 277 103 12.018996 0 - - 0 7 281 27 13.368121 0 - - 0 8 367 27 16.167744 0 - - 0 9 407 27 17.288819 0 - - 0 10 407 39 10.203526 0 - - 0 11 407 103 20.437885 0 - - 0 12 407 114 9.223513 0 - - 0 13 407 169 9.597902 0 - - 0 14 439 103 15.066733 0 - - 0 15 442 28 10.907521 0 - - 0 16 442 38 11.674077 0 - - 0 17 442 39 12.193467 0 - - 0 18 442 101 10.786363 0 - - 0 19 442 103 22.652471 0 - - 0 20 454 27 19.382976 0 - - 0 21 454 38 9.506789 0 - - 0 22 454 39 11.772219 0 - - 0 23 454 105 9.860801 0 - - 0 24 454 114 12.453117 0 - - 0 25 454 158 10.282013 0 - - 0 26 454 169 13.243201 0 - - 0 27 531 39 9.065809 0 - - 0 28 532 6 10.010737 0 - - 0 29 532 27 21.161680 0 - - 0 30 532 38 11.960678 0 - - 0 31 532 39 12.309598 0 - - 0 32 532 103 22.170305 0 - - 0 33 532 105 11.677366 0 - - 0 34 532 114 10.946309 0 - - 0 35 532 158 11.112603 0 - - 0 36 532 169 11.978170 0 - - 0 37 540 27 9.138894 0 - - 0 38 541 27 11.757371 0 - - 0 39 543 27 16.073500 0 - - 0 #12 PF00164 PF00380 272 24 268.014074 family 1, PF00164: Ribosomal protein S12 family 2, PF00380: Ribosomal protein S9/S16 index pos1 pos2 score npdbs avgdist mindist nshort 0 38 372 15.476817 1 66.6694 66.6694 0 1 106 372 12.405480 1 62.6362 62.6362 0 2 109 340 13.462260 1 101.1461 101.1461 0 3 111 340 17.766079 1 94.0037 94.0037 0 4 111 345 15.154422 1 86.7165 86.7165 0 5 111 353 12.618704 1 68.6724 68.6724 0 6 111 372 23.277752 1 48.6370 48.6370 0 7 113 372 20.871619 1 43.1260 43.1260 0 8 121 372 15.282113 1 44.3287 44.3287 0 9 125 372 11.883653 1 56.4880 56.4880 0 10 130 372 11.729439 1 64.7735 64.7735 0 11 140 345 10.479897 1 99.4091 99.4091 0 12 140 372 17.645910 1 61.4382 61.4382 0 13 165 340 19.127184 1 98.1500 98.1500 0 14 166 13 11.010639 1 99.9263 99.9263 0 15 166 340 20.638432 1 90.8435 90.8435 0 16 166 344 10.194067 1 86.9486 86.9486 0 17 166 345 15.322510 1 84.9954 84.9954 0 18 175 353 11.210048 1 64.0180 64.0180 0 19 175 372 23.165207 1 47.5460 47.5460 0 20 183 372 13.537217 1 56.3610 56.3610 0 21 203 340 12.303916 1 102.3027 102.3027 0 22 206 340 13.919658 1 97.0179 97.0179 0 23 207 340 10.275933 1 105.5467 105.5467 0 $13 PF01208 PF02607 101 18 264.624303 family 1, PF01208: Uroporphyrinogen decarboxylase (URO-D) family 2, PF02607: B12 binding domain How a protein binds B12: A 3.0 A X-ray structure of index pos1 pos2 score npdbs avgdist mindist nshort 0 74 30 23.875935 0 - - 0 1 74 68 10.052764 0 - - 0 2 152 30 9.860278 0 - - 0 3 166 30 12.532192 0 - - 0 4 168 30 15.338223 0 - - 0 5 184 51 10.085679 0 - - 0 6 222 30 17.296003 0 - - 0 7 345 30 17.388025 0 - - 0 8 367 30 16.314433 0 - - 0 9 425 83 9.786900 0 - - 0 10 454 30 12.601436 0 - - 0 11 463 30 12.864690 0 - - 0 12 531 30 17.067307 0 - - 0 13 597 30 9.882669 0 - - 0 14 604 30 22.947040 0 - - 0 15 681 30 16.289325 0 - - 0 16 685 30 12.476209 0 - - 0 17 757 30 17.965209 0 - - 0 #14 PF00037 PF01512 164 21 256.176482 family 1, PF00037: 4Fe-4S binding domain family 2, PF01512: Respiratory-chain NADH dehydrogenase 51 Kd subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 105 52 15.026183 0 - - 0 1 105 54 17.091073 0 - - 0 2 105 137 33.531837 0 - - 0 3 105 261 9.889833 0 - - 0 4 105 262 17.934863 0 - - 0 5 105 270 12.119787 0 - - 0 6 105 388 19.929218 0 - - 0 7 106 54 20.628842 0 - - 0 8 106 71 13.802741 0 - - 0 9 106 137 34.395840 0 - - 0 10 106 143 26.584272 0 - - 0 11 106 181 11.006202 0 - - 0 12 106 261 15.065866 0 - - 0 13 106 265 16.687906 0 - - 0 14 106 267 10.892910 0 - - 0 15 106 269 14.721094 0 - - 0 16 106 270 14.902711 0 - - 0 17 106 281 13.512689 0 - - 0 18 106 327 10.888470 0 - - 0 19 106 335 10.680619 0 - - 0 20 106 388 21.921462 0 - - 0 *15 PF04539 PF04542 289 15 247.920201 family 1, PF04539: Sigma-70 region 3 Structure of the bacterial RNA polymerase promoter family 2, PF04542: Sigma-70 region 2 Structure of the bacterial RNA polymerase promoter index pos1 pos2 score npdbs avgdist mindist nshort 0 6 130 29.951928 2 12.4058 8.8963 1 1 7 65 21.234114 2 21.9689 20.1649 0 2 8 77 15.566295 2 22.5342 19.4061 0 3 15 66 30.598263 2 26.4440 21.3425 0 4 15 77 23.045917 2 28.3462 24.4621 0 5 15 134 9.330289 2 14.7738 14.3380 0 6 26 65 12.777327 2 33.8909 33.0608 0 7 56 130 28.309977 2 17.5248 16.0138 0 8 62 130 24.803383 2 13.0845 11.7176 0 9 86 121 12.533240 2 24.0335 12.5106 0 10 90 65 20.695175 2 27.7805 26.3676 0 11 90 119 13.202315 2 24.4569 14.2020 0 12 90 121 28.742405 2 23.7268 14.8268 0 13 90 130 30.919501 2 20.3029 13.2256 0 14 95 77 9.967514 2 31.2117 19.4236 0 *16 PF00350 PF01031 72 37 245.335311 family 1, PF00350: Dynamin family Dynamin GTPase, a force-generating molecular switch. family 2, PF01031: Dynamin central region index pos1 pos2 score npdbs avgdist mindist nshort 0 18 34 14.205045 0 - - 0 1 18 262 10.639711 0 - - 0 2 18 514 10.613271 0 - - 0 3 18 718 9.083284 0 - - 0 4 39 262 12.533673 0 - - 0 5 39 398 11.634135 0 - - 0 6 39 479 15.040531 0 - - 0 7 39 514 12.486202 0 - - 0 8 39 517 10.895271 0 - - 0 9 39 716 12.189425 0 - - 0 10 39 718 12.165943 0 - - 0 11 39 720 14.291297 0 - - 0 12 45 34 10.751033 0 - - 0 13 295 34 12.418340 0 - - 0 14 317 261 11.971382 0 - - 0 15 317 262 11.574976 0 - - 0 16 323 6 9.474245 0 - - 0 17 323 10 12.712384 0 - - 0 18 323 262 15.258363 0 - - 0 19 323 398 13.266533 0 - - 0 20 323 514 14.832074 0 - - 0 21 323 517 13.645458 0 - - 0 22 323 716 13.110066 0 - - 0 23 329 34 10.710205 0 - - 0 24 330 34 14.409064 0 - - 0 25 330 262 10.932403 0 - - 0 26 330 276 10.713085 0 - - 0 27 330 514 10.240993 0 - - 0 28 330 716 9.679690 0 - - 0 29 330 718 10.216311 0 - - 0 30 330 720 10.910518 0 - - 0 31 342 479 9.322304 0 - - 0 32 449 262 9.493720 0 - - 0 33 476 37 11.679993 0 - - 0 34 536 34 9.246328 0 - - 0 35 539 37 10.543483 0 - - 0 36 572 37 9.306380 0 - - 0 *17 PF02310 PF02965 104 20 240.738641 family 1, PF02310: B12 binding domain How a protein prepares for B12 binding: structure and family 2, PF02965: Vitamin B12 dependent methionine synthase, activation domain The structure of the C-terminal domain of methionine index pos1 pos2 score npdbs avgdist mindist nshort 0 46 27 23.659126 0 - - 0 1 46 38 13.957035 0 - - 0 2 46 39 15.308653 0 - - 0 3 46 103 27.512545 0 - - 0 4 46 104 9.379540 0 - - 0 5 46 105 15.687687 0 - - 0 6 46 114 16.830677 0 - - 0 7 46 158 14.136662 0 - - 0 8 46 167 9.188494 0 - - 0 9 46 169 17.812126 0 - - 0 10 121 27 13.333297 0 - - 0 11 121 103 17.135984 0 - - 0 12 158 27 9.935201 0 - - 0 13 171 27 15.660432 0 - - 0 14 171 105 9.853324 0 - - 0 15 173 27 13.960217 0 - - 0 16 173 103 12.956915 0 - - 0 17 179 6 9.481776 0 - - 0 18 181 6 9.195488 0 - - 0 19 210 27 14.075464 0 - - 0 #18 PF00318 PF00411 311 27 237.121970 family 1, PF00318: Ribosomal protein S2 family 2, PF00411: Ribosomal protein S11 index pos1 pos2 score npdbs avgdist mindist nshort 0 9 38 20.423519 1 76.6529 76.6529 0 1 9 40 24.962955 1 71.4112 71.4112 0 2 9 55 16.780000 1 66.0931 66.0931 0 3 9 99 18.025205 1 55.5880 55.5880 0 4 9 152 13.921916 1 59.1562 59.1562 0 5 122 40 11.635414 1 69.0088 69.0088 0 6 189 40 11.989441 1 68.1326 68.1326 0 7 189 55 10.116839 1 65.1844 65.1844 0 8 189 99 10.438342 1 57.6841 57.6841 0 9 192 38 16.256545 1 74.1371 74.1371 0 10 192 40 21.553409 1 68.6978 68.6978 0 11 192 44 9.684026 1 67.4691 67.4691 0 12 192 48 12.962504 1 66.8205 66.8205 0 13 192 55 13.884711 1 66.2883 66.2883 0 14 192 99 17.717467 1 58.9642 58.9642 0 15 192 145 14.995059 1 63.7546 63.7546 0 16 192 147 10.444471 1 60.2372 60.2372 0 17 192 152 9.970263 1 57.8800 57.8800 0 18 267 38 13.173119 1 83.0882 83.0882 0 19 267 40 16.517246 1 77.0456 77.0456 0 20 267 99 13.229124 1 67.2854 67.2854 0 21 358 38 20.390976 1 81.8228 81.8228 0 22 378 38 23.995043 1 75.0403 75.0403 0 23 378 40 29.317574 1 69.6433 69.6433 0 24 378 55 19.599925 1 64.4871 64.4871 0 25 378 99 18.725338 1 54.5412 54.5412 0 26 378 152 13.499732 1 58.2943 58.2943 0 19 PF01432 PF02347 128 26 235.436618 family 1, PF01432: Peptidase family M3 Evolutionary families of metallopeptidases. family 2, PF02347: Glycine cleavage system P-protein Genetics of the synthesis of serine from glycine and the index pos1 pos2 score npdbs avgdist mindist nshort 0 739 2 10.193507 0 - - 0 1 739 5 10.408923 0 - - 0 2 739 164 12.192771 0 - - 0 3 739 219 10.502714 0 - - 0 4 739 233 13.739851 0 - - 0 5 739 234 9.967307 0 - - 0 6 739 237 9.818403 0 - - 0 7 739 287 13.728226 0 - - 0 8 739 316 11.148640 0 - - 0 9 739 430 16.888734 0 - - 0 10 739 573 9.061635 0 - - 0 11 739 591 12.238601 0 - - 0 12 739 727 12.764935 0 - - 0 13 739 786 17.105744 0 - - 0 14 739 807 11.739657 0 - - 0 15 739 880 9.717156 0 - - 0 16 739 884 12.606508 0 - - 0 17 746 430 11.995723 0 - - 0 18 746 786 10.272385 0 - - 0 19 1009 233 10.966498 0 - - 0 20 1009 234 9.424704 0 - - 0 21 1009 430 14.436485 0 - - 0 22 1009 727 10.013740 0 - - 0 23 1030 430 9.759451 0 - - 0 24 1205 430 12.056220 0 - - 0 25 1205 786 9.860969 0 - - 0 *20 PF03463 PF03464 94 51 231.596645 family 1, PF03463: eRF1 domain 1 The crystal structure of human eukaryotic release factor family 2, PF03464: eRF1 domain 2 The crystal structure of human eukaryotic release factor index pos1 pos2 score npdbs avgdist mindist nshort 0 12 12 14.291025 0 - - 0 1 12 37 9.904431 0 - - 0 2 30 62 9.888721 0 - - 0 3 30 69 9.655821 0 - - 0 4 30 107 9.175301 0 - - 0 5 30 125 13.051505 0 - - 0 6 30 184 11.136271 0 - - 0 7 31 3 11.504823 0 - - 0 8 31 8 11.228752 0 - - 0 9 31 10 12.246202 0 - - 0 10 31 12 11.166146 0 - - 0 11 31 69 14.081091 0 - - 0 12 31 107 12.441382 0 - - 0 13 31 111 9.231379 0 - - 0 14 88 69 9.818772 0 - - 0 15 88 125 13.600042 0 - - 0 16 101 62 10.864518 0 - - 0 17 101 69 10.311484 0 - - 0 18 173 64 12.474864 0 - - 0 19 173 70 10.038523 0 - - 0 20 185 3 10.600111 0 - - 0 21 185 8 10.294012 0 - - 0 22 185 10 10.903551 0 - - 0 23 185 12 9.568561 0 - - 0 24 185 69 13.464255 0 - - 0 25 185 107 11.432444 0 - - 0 26 185 125 16.437195 0 - - 0 27 185 144 10.064629 0 - - 0 28 186 45 9.312660 0 - - 0 29 186 62 18.360846 0 - - 0 30 186 66 12.649290 0 - - 0 31 186 126 14.470331 0 - - 0 32 186 144 14.190607 0 - - 0 33 201 62 12.554448 0 - - 0 34 201 107 9.201165 0 - - 0 35 215 107 9.590880 0 - - 0 36 247 3 14.800958 0 - - 0 37 247 8 13.085541 0 - - 0 38 247 10 13.236578 0 - - 0 39 247 12 13.552304 0 - - 0 40 247 37 10.001650 0 - - 0 41 247 62 18.796698 0 - - 0 42 247 64 13.802096 0 - - 0 43 247 66 12.828291 0 - - 0 44 247 69 18.499015 0 - - 0 45 247 72 11.005524 0 - - 0 46 247 107 14.626334 0 - - 0 47 247 111 10.466620 0 - - 0 48 247 126 13.329244 0 - - 0 49 247 144 13.234770 0 - - 0 50 247 182 9.960296 0 - - 0 21 PF01512 PF02554 59 72 230.608637 family 1, PF01512: Respiratory-chain NADH dehydrogenase 51 Kd subunit family 2, PF02554: Carbon starvation protein CstA Molecular and functional characterization of a carbon index pos1 pos2 score npdbs avgdist mindist nshort 0 1 54 11.323945 0 - - 0 1 1 463 11.822585 0 - - 0 2 51 649 13.377891 0 - - 0 3 54 649 16.263328 0 - - 0 4 71 649 14.873630 0 - - 0 5 131 649 13.692250 0 - - 0 6 137 58 13.549399 0 - - 0 7 137 61 15.347471 0 - - 0 8 137 79 9.154123 0 - - 0 9 137 109 16.009369 0 - - 0 10 137 615 10.744516 0 - - 0 11 137 618 14.471265 0 - - 0 12 137 632 15.446637 0 - - 0 13 137 649 24.930468 0 - - 0 14 140 62 11.174361 0 - - 0 15 140 469 9.427854 0 - - 0 16 150 649 9.724885 0 - - 0 17 166 471 9.438339 0 - - 0 18 166 649 13.914670 0 - - 0 19 180 649 15.340201 0 - - 0 20 181 649 14.080218 0 - - 0 21 257 61 10.372643 0 - - 0 22 257 74 9.848790 0 - - 0 23 257 109 9.988292 0 - - 0 24 257 471 14.073480 0 - - 0 25 257 618 9.417000 0 - - 0 26 257 649 19.704147 0 - - 0 27 261 471 9.725765 0 - - 0 28 261 649 14.070261 0 - - 0 29 264 6 9.663363 0 - - 0 30 264 19 9.905870 0 - - 0 31 264 61 9.589424 0 - - 0 32 264 74 9.116406 0 - - 0 33 264 109 9.644219 0 - - 0 34 264 471 11.468844 0 - - 0 35 264 632 9.821021 0 - - 0 36 264 649 19.573837 0 - - 0 37 265 54 9.024976 0 - - 0 38 265 61 10.247306 0 - - 0 39 265 471 13.464635 0 - - 0 40 265 618 9.472728 0 - - 0 41 265 649 19.411530 0 - - 0 42 267 649 13.289470 0 - - 0 43 269 649 13.798736 0 - - 0 44 270 471 10.071920 0 - - 0 45 270 649 16.101170 0 - - 0 46 281 471 10.752822 0 - - 0 47 281 649 15.608223 0 - - 0 48 290 649 16.243012 0 - - 0 49 324 471 10.685714 0 - - 0 50 324 649 16.054651 0 - - 0 51 327 649 13.247515 0 - - 0 52 332 649 9.314455 0 - - 0 53 333 54 9.281589 0 - - 0 54 333 61 11.194865 0 - - 0 55 333 469 9.218817 0 - - 0 56 333 471 13.893333 0 - - 0 57 333 618 9.968062 0 - - 0 58 333 649 21.109791 0 - - 0 59 335 649 14.276717 0 - - 0 60 377 649 10.879386 0 - - 0 61 388 54 10.946610 0 - - 0 62 388 61 12.767270 0 - - 0 63 388 109 13.369616 0 - - 0 64 388 463 10.268114 0 - - 0 65 388 469 10.612236 0 - - 0 66 388 471 15.806207 0 - - 0 67 388 475 10.536340 0 - - 0 68 388 617 9.884196 0 - - 0 69 388 618 11.446364 0 - - 0 70 388 632 12.382928 0 - - 0 71 388 649 21.800545 0 - - 0 *22 PF01642 PF02310 77 36 229.137246 family 1, PF01642: Methylmalonyl-CoA mutase How coenzyme B12 radicals are generated: the crystal family 2, PF02310: B12 binding domain How a protein prepares for B12 binding: structure and index pos1 pos2 score npdbs avgdist mindist nshort 0 54 14 10.071419 1 33.8822 33.8822 0 1 71 0 10.704124 1 53.1768 53.1768 0 2 71 14 10.388839 1 33.9608 33.9608 0 3 92 0 16.304303 1 42.3089 42.3089 0 4 92 14 16.056716 1 21.3194 21.3194 0 5 92 68 23.003956 1 35.5448 35.5448 0 6 92 146 9.608854 1 40.0449 40.0449 0 7 133 0 16.334260 1 28.6916 28.6916 0 8 133 14 15.621797 1 2.8133 2.8133 1 9 144 14 14.951983 1 5.0194 5.0194 1 10 190 68 12.182209 1 38.6474 38.6474 0 11 194 68 12.562275 1 28.0873 28.0873 0 12 200 0 20.027777 1 42.1326 42.1326 0 13 381 68 13.409130 1 17.7582 17.7582 0 14 383 68 14.135750 1 17.6035 17.6035 0 15 440 68 9.951522 1 22.9075 22.9075 0 16 532 14 9.317245 1 22.8895 22.8895 0 17 539 14 14.252449 1 30.5481 30.5481 0 18 600 146 9.907435 1 44.7166 44.7166 0 19 613 68 13.186065 1 30.7094 30.7094 0 20 666 0 12.613471 1 44.7449 44.7449 0 21 666 14 11.821689 1 27.2131 27.2131 0 22 666 45 11.141586 1 40.0335 40.0335 0 23 667 0 11.103520 1 47.0639 47.0639 0 24 667 14 10.443223 1 30.0006 30.0006 0 25 667 45 9.764629 1 42.2644 42.2644 0 26 667 68 16.498230 1 41.6770 41.6770 0 27 673 0 9.835495 1 51.8815 51.8815 0 28 673 14 9.393307 1 33.1053 33.1053 0 29 673 68 15.302367 1 45.3778 45.3778 0 30 745 68 9.968555 1 13.5895 13.5895 0 31 753 68 21.976594 1 15.8887 15.8887 0 32 760 68 9.624067 1 17.9686 17.9686 0 33 827 14 9.751962 1 10.1779 10.1779 0 34 838 0 14.230088 1 37.7242 37.7242 0 35 966 156 11.876832 1 23.9779 23.9779 0 *23 PF00679 PF03764 327 11 211.634825 family 1, PF00679: Elongation factor G C-terminus family 2, PF03764: Elongation factor G, domain IV index pos1 pos2 score npdbs avgdist mindist nshort 0 74 224 33.711137 1 38.6119 38.6119 0 1 405 147 13.858303 1 39.4997 39.4997 0 2 405 211 13.615998 1 46.4495 46.4495 0 3 405 213 22.220913 1 44.0973 44.0973 0 4 405 220 9.784266 1 37.5430 37.5430 0 5 405 224 13.007526 1 33.1431 33.1431 0 6 408 211 13.309156 1 50.7955 50.7955 0 7 408 213 19.697582 1 48.5716 48.5716 0 8 408 224 10.780664 1 37.7286 37.7286 0 9 409 133 53.959561 0 - - 0 10 409 152 37.469035 1 43.4531 43.4531 0 *24 PF00208 PF02812 169 16 195.948264 family 1, PF00208: Glutamate/Leucine/Phenylalanine/Valine dehydrogenase A role for quaternary structure in the substrate family 2, PF02812: Glu/Leu/Phe/Val dehydrogenase, dimerisation domain A role for quaternary structure in the substrate index pos1 pos2 score npdbs avgdist mindist nshort 0 141 65 19.909623 8 19.7776 15.5818 0 1 141 70 15.163814 8 19.5757 17.8855 0 2 141 155 10.705225 8 18.1969 15.3604 0 3 141 169 11.516704 8 32.7995 29.8438 0 4 373 155 14.384417 8 22.4998 20.1935 0 5 380 65 21.583821 8 9.9246 7.3697 5 6 380 155 9.728104 8 14.6221 12.2800 0 7 380 169 10.532107 8 29.6097 26.1915 0 8 432 65 33.728776 8 10.0621 3.2685 2 9 432 131 18.454769 8 28.3122 21.2298 0 10 432 155 19.691641 8 14.8913 12.4984 0 11 432 169 20.308470 8 30.3664 26.6263 0 12 433 43 9.147751 8 18.4124 16.0287 0 13 433 151 22.382391 8 23.0858 18.1080 0 14 478 171 11.352395 8 14.8697 14.4938 0 15 482 155 10.718876 8 12.0372 11.5281 0 *25 PF01031 PF02212 69 21 193.553792 family 1, PF01031: Dynamin central region family 2, PF02212: Dynamin GTPase effector domain index pos1 pos2 score npdbs avgdist mindist nshort 0 18 17 11.198373 0 - - 0 1 34 39 11.688146 0 - - 0 2 114 68 11.441647 0 - - 0 3 151 68 13.894691 0 - - 0 4 195 17 11.080464 0 - - 0 5 195 68 15.147467 0 - - 0 6 262 39 9.745603 0 - - 0 7 262 68 16.039883 0 - - 0 8 271 68 14.904670 0 - - 0 9 276 68 14.378113 0 - - 0 10 379 26 10.259670 0 - - 0 11 435 17 11.508567 0 - - 0 12 465 17 12.649101 0 - - 0 13 479 17 13.191656 0 - - 0 14 514 17 11.827676 0 - - 0 15 518 17 12.019540 0 - - 0 16 711 17 9.254145 0 - - 0 17 718 17 10.761679 0 - - 0 18 718 68 16.069529 0 - - 0 19 720 17 10.271738 0 - - 0 20 720 68 16.233369 0 - - 0 #26 PF00177 PF00411 318 23 193.172107 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF00411: Ribosomal protein S11 index pos1 pos2 score npdbs avgdist mindist nshort 0 62 38 13.676281 1 44.6151 44.6151 0 1 304 38 12.954484 1 22.5295 22.5295 0 2 304 40 18.803823 1 18.1003 18.1003 0 3 304 44 9.263596 1 16.8970 16.8970 0 4 304 141 16.010969 1 37.1261 37.1261 0 5 304 144 9.883608 1 37.1518 37.1518 0 6 304 147 9.576630 1 29.5415 29.5415 0 7 304 152 9.651071 1 25.5114 25.5114 0 8 323 40 11.350001 1 10.8224 10.8224 0 9 324 38 13.345689 1 18.5570 18.5570 0 10 324 40 17.078940 1 12.3780 12.3780 0 11 324 48 10.110125 1 15.0324 15.0324 0 12 324 99 14.871696 1 18.3141 18.3141 0 13 330 40 12.907582 1 16.7631 16.7631 0 14 340 141 11.261945 1 53.4119 53.4119 0 15 343 141 21.313541 1 57.8134 57.8134 0 16 344 38 9.586274 1 27.4878 27.4878 0 17 344 40 13.337268 1 22.2353 22.2353 0 18 344 141 11.734870 1 54.6871 54.6871 0 19 344 152 9.668615 1 46.9757 46.9757 0 20 416 38 9.751164 1 18.0754 18.0754 0 21 416 40 14.611987 1 12.9365 12.9365 0 22 416 99 12.851470 1 24.1691 24.1691 0 *27 PF02878 PF02880 250 9 191.647360 family 1, PF02878: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I The crystal structure of muscle phosphoglucomutase refined family 2, PF02880: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III The crystal structure of muscle phosphoglucomutase refined index pos1 pos2 score npdbs avgdist mindist nshort 0 3 6 11.841703 3 24.2091 22.7967 0 1 3 209 13.074800 3 21.8560 20.1971 0 2 6 85 30.104074 3 14.2541 12.2562 0 3 6 124 48.050818 3 6.4802 5.6136 3 4 171 260 15.856061 3 5.6087 3.5120 3 5 262 124 44.784448 3 8.8297 8.0241 2 6 277 85 25.342124 3 15.1203 13.9953 0 7 277 124 43.767899 3 5.4174 4.1762 3 8 277 259 31.740228 3 5.0520 3.4084 3 *28 PF00670 PF05221 175 30 180.857110 family 1, PF00670: S-adenosyl-L-homocysteine hydrolase, NAD binding domain family 2, PF05221: S-adenosyl-L-homocysteine hydrolase index pos1 pos2 score npdbs avgdist mindist nshort 0 4 106 14.585724 3 18.0196 17.0733 0 1 4 307 10.476952 3 7.9062 5.8288 3 2 5 95 10.680126 3 27.6248 27.0226 0 3 5 106 14.735124 3 21.8119 20.8149 0 4 5 307 11.343589 3 7.7036 6.4941 3 5 9 101 9.438006 3 21.4918 20.3952 0 6 9 106 11.467843 3 18.8423 16.9915 0 7 9 306 13.878344 3 13.5184 12.6706 0 8 9 307 9.256129 3 13.3070 11.1398 0 9 66 59 11.259993 3 19.9345 14.9746 0 10 66 95 16.203555 3 26.1479 25.9172 0 11 66 103 9.007004 3 22.0497 21.0112 0 12 66 104 11.825801 3 18.1814 17.1075 0 13 66 106 21.184828 3 22.8859 21.8431 0 14 66 107 12.701486 3 22.1735 21.0261 0 15 66 113 12.875326 3 25.8559 25.0761 0 16 66 298 9.124405 3 10.4263 9.8816 1 17 66 306 23.631013 3 3.7239 3.3115 3 18 66 307 20.072744 3 3.7660 2.8125 3 19 66 558 14.649154 3 15.7639 15.6121 0 20 66 570 20.192298 3 20.7293 20.3769 0 21 66 622 9.759607 3 14.8068 14.2727 0 22 66 663 18.975185 3 17.2369 16.3734 0 23 66 675 12.733990 3 14.4675 14.3920 0 24 80 106 9.685441 3 18.8171 17.6529 0 25 216 306 11.557469 3 11.8604 11.3815 0 26 216 307 9.688481 3 13.1870 11.5922 0 27 267 106 12.352464 3 8.6121 6.0032 2 28 267 306 12.471208 3 24.2473 22.9821 0 29 267 307 13.534128 3 25.4272 23.1930 0 $29 PF01407 PF01440 75 13 178.908994 family 1, PF01407: Geminivirus AL3 protein Molecular characterization of the AL3 protein encoded by a family 2, PF01440: Geminivirus AL2 protein Transactivation in a geminivirus: AL2 gene product is index pos1 pos2 score npdbs avgdist mindist nshort 0 47 50 14.474851 0 - - 0 1 47 160 35.792658 0 - - 0 2 59 160 47.511148 0 - - 0 3 71 133 11.089136 0 - - 0 4 82 160 32.030921 0 - - 0 5 92 155 15.343633 0 - - 0 6 100 160 27.175061 0 - - 0 7 106 160 22.226331 0 - - 0 8 109 160 38.440446 0 - - 0 9 113 160 34.027687 0 - - 0 10 140 160 27.134252 0 - - 0 11 145 15 13.959484 0 - - 0 12 145 160 35.105479 0 - - 0 $30 PF03135 PF04610 60 23 176.025552 family 1, PF03135: CagE, TrbE, VirB family, component of type IV transporter system Virulence factors of Helicobacter pylori responsible for family 2, PF04610: TrbL/VirB6 plasmid conjugal transfer protein Essential components of the Ti plasmid trb system, a type index pos1 pos2 score npdbs avgdist mindist nshort 0 2 342 9.145782 0 - - 0 1 114 324 18.523858 0 - - 0 2 114 339 15.483368 0 - - 0 3 114 342 18.386351 0 - - 0 4 119 342 16.604009 0 - - 0 5 137 324 16.037441 0 - - 0 6 137 339 12.641881 0 - - 0 7 137 342 16.145300 0 - - 0 8 139 324 10.916960 0 - - 0 9 139 342 11.538046 0 - - 0 10 173 324 12.550674 0 - - 0 11 173 342 13.133343 0 - - 0 12 185 324 14.182353 0 - - 0 13 185 339 11.689551 0 - - 0 14 185 342 14.563879 0 - - 0 15 219 324 12.607942 0 - - 0 16 219 342 12.839417 0 - - 0 17 232 324 20.227827 0 - - 0 18 232 339 17.830309 0 - - 0 19 232 342 20.275127 0 - - 0 20 326 324 16.521503 0 - - 0 21 326 339 13.280920 0 - - 0 22 326 342 16.603490 0 - - 0 *31 PF02607 PF02965 103 27 174.470091 family 1, PF02607: B12 binding domain How a protein binds B12: A 3.0 A X-ray structure of family 2, PF02965: Vitamin B12 dependent methionine synthase, activation domain The structure of the C-terminal domain of methionine index pos1 pos2 score npdbs avgdist mindist nshort 0 31 27 13.811970 0 - - 0 1 51 27 11.029738 0 - - 0 2 51 103 12.226514 0 - - 0 3 53 101 9.147982 0 - - 0 4 71 6 12.369748 0 - - 0 5 71 27 14.813165 0 - - 0 6 71 28 10.165931 0 - - 0 7 71 38 11.900288 0 - - 0 8 71 39 9.120037 0 - - 0 9 71 158 9.024053 0 - - 0 10 74 6 13.221533 0 - - 0 11 74 27 17.303043 0 - - 0 12 74 28 13.036306 0 - - 0 13 74 31 9.284661 0 - - 0 14 74 38 13.198813 0 - - 0 15 74 39 10.802522 0 - - 0 16 74 158 11.371294 0 - - 0 17 76 27 9.639683 0 - - 0 18 77 27 10.706724 0 - - 0 19 77 103 13.333895 0 - - 0 20 80 27 17.879549 0 - - 0 21 80 38 10.570022 0 - - 0 22 80 39 11.050967 0 - - 0 23 80 103 21.074612 0 - - 0 24 80 114 10.820274 0 - - 0 25 80 158 9.513804 0 - - 0 26 80 169 12.953883 0 - - 0 *32 PF01493 PF01645 123 30 173.882394 family 1, PF01493: GXGXG motif The formylmethanofuran dehydrogenase isoenzymes in family 2, PF01645: Conserved region in glutamate synthase Sequence of the GLT1 gene from Saccharomyces cerevisiae index pos1 pos2 score npdbs avgdist mindist nshort 0 12 553 10.631263 2 33.8161 33.4121 0 1 15 209 9.289188 2 34.0060 33.7824 0 2 15 324 13.771009 2 18.4142 18.2003 0 3 15 641 13.002408 2 43.2569 43.1692 0 4 77 667 9.454248 2 38.2106 37.9922 0 5 82 667 9.812475 2 29.2486 29.1607 0 6 131 216 11.994496 2 31.7779 31.6649 0 7 131 571 13.164147 2 25.1537 24.9923 0 8 131 641 12.435553 2 39.0378 38.7729 0 9 131 667 17.357614 2 29.5106 29.3404 0 10 131 894 13.184094 2 47.6665 47.5116 0 11 134 553 10.548840 2 28.8511 28.5959 0 12 135 667 14.518473 2 28.0123 27.9324 0 13 150 576 14.832291 2 50.4647 49.9379 0 14 266 4 13.899882 2 47.5032 46.2329 0 15 266 184 11.468423 2 33.6290 33.1778 0 16 266 553 14.246425 2 33.8305 33.4700 0 17 266 667 13.970846 2 35.4360 35.3192 0 18 279 4 15.485385 2 41.4021 39.8627 0 19 279 567 11.226423 2 25.1836 25.0852 0 20 279 667 14.294854 2 31.0785 30.9211 0 21 398 180 11.416621 2 38.6427 38.2378 0 22 398 255 12.377677 2 27.6724 27.3886 0 23 398 324 11.537944 2 23.9526 23.6199 0 24 398 576 19.073916 2 35.8525 35.3115 0 25 398 853 13.566634 2 39.1292 38.9177 0 26 398 879 14.495239 2 46.3959 46.1835 0 27 448 216 9.361486 2 35.7790 35.5882 0 28 448 567 13.053392 2 21.5046 21.3857 0 29 462 576 16.707235 2 49.4467 47.6046 0 *33 PF02574 PF02965 104 19 171.675443 family 1, PF02574: Homocysteine S-methyltransferase S-methylmethionine metabolism in Escherichia coli. family 2, PF02965: Vitamin B12 dependent methionine synthase, activation domain The structure of the C-terminal domain of methionine index pos1 pos2 score npdbs avgdist mindist nshort 0 102 27 21.948093 0 - - 0 1 329 27 18.507600 0 - - 0 2 329 38 11.767439 0 - - 0 3 329 114 12.018321 0 - - 0 4 329 158 12.744255 0 - - 0 5 329 169 13.049397 0 - - 0 6 439 27 24.134352 0 - - 0 7 439 38 18.333717 0 - - 0 8 439 114 13.292337 0 - - 0 9 439 158 13.469316 0 - - 0 10 439 167 9.270189 0 - - 0 11 439 169 16.331819 0 - - 0 12 613 27 16.557633 0 - - 0 13 613 38 10.042631 0 - - 0 14 689 27 14.060968 0 - - 0 15 699 101 10.427684 0 - - 0 16 816 103 12.785926 0 - - 0 17 829 28 11.968145 0 - - 0 18 829 38 12.799227 0 - - 0 #34 PF02310 PF02574 115 23 169.659340 family 1, PF02310: B12 binding domain How a protein prepares for B12 binding: structure and family 2, PF02574: Homocysteine S-methyltransferase S-methylmethionine metabolism in Escherichia coli. index pos1 pos2 score npdbs avgdist mindist nshort 0 39 102 9.557123 0 - - 0 1 40 102 12.190999 0 - - 0 2 46 102 34.743252 0 - - 0 3 46 104 13.912936 0 - - 0 4 46 329 29.341250 0 - - 0 5 46 439 21.092565 0 - - 0 6 46 613 18.163082 0 - - 0 7 46 689 16.435855 0 - - 0 8 71 102 9.657666 0 - - 0 9 121 329 17.893009 0 - - 0 10 121 439 14.660758 0 - - 0 11 121 613 9.731534 0 - - 0 12 158 102 12.317821 0 - - 0 13 158 329 12.095689 0 - - 0 14 158 439 10.089411 0 - - 0 15 159 439 9.745185 0 - - 0 16 171 102 21.167922 0 - - 0 17 171 329 20.472941 0 - - 0 18 171 439 17.768644 0 - - 0 19 171 613 13.215668 0 - - 0 20 171 689 10.807732 0 - - 0 21 210 329 15.644363 0 - - 0 22 210 613 11.162888 0 - - 0 #35 PF00177 PF00318 314 15 158.794030 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF00318: Ribosomal protein S2 index pos1 pos2 score npdbs avgdist mindist nshort 0 97 192 12.012153 1 71.3420 71.3420 0 1 97 267 12.786985 1 73.3015 73.3015 0 2 281 192 9.479313 1 60.2493 60.2493 0 3 304 189 10.143975 1 52.8312 52.8312 0 4 304 192 16.635374 1 52.7179 52.7179 0 5 304 267 11.717312 1 62.4893 62.4893 0 6 304 358 17.890047 1 63.8917 63.8917 0 7 323 358 13.566081 1 72.2602 72.2602 0 8 324 267 9.833542 1 65.5711 65.5711 0 9 324 358 16.395160 1 68.6053 68.6053 0 10 330 192 9.978474 1 57.6175 57.6175 0 11 343 4 19.695503 1 81.0256 81.0256 0 12 344 358 11.902482 1 80.3322 80.3322 0 13 416 9 10.417062 1 73.0588 73.0588 0 14 416 192 10.768946 1 67.9221 67.9221 0 *36 PF01357 PF03330 59 18 157.083823 family 1, PF01357: Pollen allergen Complete primary structure of a Lolium perenne (perennial family 2, PF03330: Rare lipoprotein A (RlpA)-like double-psi beta-barrel Multicopy suppressors of prc mutant Escherichia coli index pos1 pos2 score npdbs avgdist mindist nshort 0 1 100 12.675479 1 18.1823 18.1823 0 1 1 165 10.426271 1 30.6454 30.6454 0 2 3 100 15.059030 1 16.5972 16.5972 0 3 3 101 10.792784 1 20.1030 20.1030 0 4 3 132 9.637648 1 29.7058 29.7058 0 5 3 165 11.800503 1 35.1675 35.1675 0 6 12 100 9.985003 1 26.8839 26.8839 0 7 14 100 12.862708 1 21.0532 21.0532 0 8 14 165 10.694382 1 43.6927 43.6927 0 9 19 100 11.686052 1 14.2362 14.2362 0 10 20 100 11.984591 1 15.2440 15.2440 0 11 24 165 9.206872 1 29.2235 29.2235 0 12 34 100 11.377240 1 32.1475 32.1475 0 13 35 100 11.788538 1 34.2051 34.2051 0 14 37 100 9.147327 1 35.2193 35.2193 0 15 58 100 11.923937 1 13.4153 13.4153 0 16 58 101 9.592819 1 15.8602 15.8602 0 17 65 132 9.006275 1 24.4702 24.4702 0 *37 PF02847 PF02854 47 18 153.559249 family 1, PF02847: MA3 domain Novel eIF4G domain homologues linking mRNA translation with family 2, PF02854: MIF4G domain Novel eIF4G domain homologues linking mRNA translation with index pos1 pos2 score npdbs avgdist mindist nshort 0 6 99 9.507826 0 - - 0 1 6 172 11.896993 0 - - 0 2 29 19 15.545062 0 - - 0 3 29 53 13.285237 0 - - 0 4 29 70 11.972518 0 - - 0 5 29 101 14.758200 0 - - 0 6 29 172 15.899430 0 - - 0 7 97 299 10.938445 0 - - 0 8 98 38 11.235443 0 - - 0 9 98 53 9.365637 0 - - 0 10 98 99 9.568632 0 - - 0 11 107 300 12.303739 0 - - 0 12 228 99 9.157725 0 - - 0 13 228 172 9.544529 0 - - 0 14 229 54 11.741164 0 - - 0 15 229 172 9.799520 0 - - 0 16 229 295 10.435444 0 - - 0 17 229 300 10.270184 0 - - 0 38 PF00316 PF03313 53 14 151.829380 family 1, PF00316: Fructose-1-6-bisphosphatase Structure of rabbit liver fructose 1,6-bisphosphatase at family 2, PF03313: Serine dehydratase alpha chain index pos1 pos2 score npdbs avgdist mindist nshort 0 8 434 10.664765 0 - - 0 1 53 434 9.703805 0 - - 0 2 205 434 10.988664 0 - - 0 3 296 434 10.242006 0 - - 0 4 326 434 12.204082 0 - - 0 5 384 434 9.847324 0 - - 0 6 397 434 11.630072 0 - - 0 7 421 434 10.175817 0 - - 0 8 422 434 10.351316 0 - - 0 9 424 434 10.103268 0 - - 0 10 432 483 9.085476 0 - - 0 11 449 434 11.993614 0 - - 0 12 473 434 12.050827 0 - - 0 13 530 434 12.788359 0 - - 0 #39 PF00203 PF00238 320 17 145.449207 family 1, PF00203: Ribosomal protein S19 family 2, PF00238: Ribosomal protein L14p/L23e index pos1 pos2 score npdbs avgdist mindist nshort 0 77 9 11.462755 0 - - 0 1 77 91 9.280617 0 - - 0 2 77 154 13.202629 0 - - 0 3 81 253 11.168648 0 - - 0 4 81 259 14.358528 0 - - 0 5 94 0 9.699778 0 - - 0 6 94 257 11.138077 0 - - 0 7 94 259 17.081704 0 - - 0 8 129 9 11.688090 0 - - 0 9 129 154 16.797641 0 - - 0 10 129 253 17.597251 0 - - 0 11 129 259 17.750451 0 - - 0 12 129 283 14.043631 0 - - 0 13 129 315 16.334084 0 - - 0 14 137 0 12.007017 0 - - 0 15 137 253 16.927657 0 - - 0 16 137 257 14.445738 0 - - 0 *40 PF02310 PF02607 120 15 130.667976 family 1, PF02310: B12 binding domain How a protein prepares for B12 binding: structure and family 2, PF02607: B12 binding domain How a protein binds B12: A 3.0 A X-ray structure of index pos1 pos2 score npdbs avgdist mindist nshort 0 8 70 9.701430 1 20.5735 20.5735 0 1 11 30 19.651871 1 33.4066 33.4066 0 2 21 30 20.615335 1 24.6139 24.6139 0 3 39 51 10.344047 1 9.4691 9.4691 1 4 40 51 11.046404 1 5.4372 5.4372 1 5 46 51 25.417197 1 11.4575 11.4575 0 6 46 55 10.725228 1 16.0989 16.0989 0 7 46 74 13.595636 1 28.8528 28.8528 0 8 46 80 19.593953 1 20.9512 20.9512 0 9 71 51 13.249667 1 18.0976 18.0976 0 10 158 51 11.433170 1 18.0268 18.0268 0 11 159 51 10.835670 1 20.8466 20.8466 0 12 159 74 10.939142 1 18.8857 18.8857 0 13 171 51 14.827498 1 22.8577 22.8577 0 14 179 71 10.342298 1 28.6823 28.6823 0 $41 PF03135 PF03524 69 15 124.118896 family 1, PF03135: CagE, TrbE, VirB family, component of type IV transporter system Virulence factors of Helicobacter pylori responsible for family 2, PF03524: Conjugal transfer protein index pos1 pos2 score npdbs avgdist mindist nshort 0 114 742 15.873026 0 - - 0 1 122 8 13.209752 0 - - 0 2 122 30 9.456306 0 - - 0 3 137 8 21.702566 0 - - 0 4 137 742 11.910497 0 - - 0 5 173 8 20.076446 0 - - 0 6 173 742 11.092735 0 - - 0 7 185 8 22.439202 0 - - 0 8 185 30 15.353949 0 - - 0 9 185 742 10.679493 0 - - 0 10 219 8 19.634294 0 - - 0 11 232 8 26.146996 0 - - 0 12 232 742 14.305284 0 - - 0 13 326 8 23.395200 0 - - 0 14 326 742 10.748285 0 - - 0 #42 PF00164 PF00253 311 10 121.777575 family 1, PF00164: Ribosomal protein S12 family 2, PF00253: Ribosomal protein S14p/S29e index pos1 pos2 score npdbs avgdist mindist nshort 0 109 60 15.174437 1 78.3091 78.3091 0 1 109 66 9.339501 1 78.2072 78.2072 0 2 111 31 13.315080 1 53.9966 53.9966 0 3 153 66 14.770306 1 80.0792 80.0792 0 4 163 60 11.876570 1 76.0353 76.0353 0 5 163 66 9.083003 1 76.4017 76.4017 0 6 165 60 20.765317 1 76.6528 76.6528 0 7 204 60 18.419531 1 75.1813 75.1813 0 8 206 60 15.493034 1 70.0396 70.0396 0 9 207 60 10.982357 1 77.1923 77.1923 0 *43 PF03144 PF03764 409 5 116.111130 family 1, PF03144: Elongation factor Tu domain 2 Crystal structure of the ternary complex of Phe-tRNAPhe, family 2, PF03764: Elongation factor G, domain IV index pos1 pos2 score npdbs avgdist mindist nshort 0 0 224 28.578927 1 73.5272 73.5272 0 1 105 224 20.514297 1 79.0173 79.0173 0 2 118 147 10.909170 1 75.7760 75.7760 0 3 118 154 24.696685 1 69.3439 69.3439 0 4 118 213 18.098763 1 79.0533 79.0533 0 *44 PF01656 PF07685 129 12 113.922113 family 1, PF01656: CobQ/CobB/MinD/ParA nucleotide binding domain Cobalamin (vitamin B12) biosynthesis: identification and family 2, PF07685: CobB/CobQ-like glutamine amidotransferase domain The synthetase domains of cobalamin biosynthesis index pos1 pos2 score npdbs avgdist mindist nshort 0 59 37 11.619895 0 - - 0 1 67 234 9.805315 0 - - 0 2 148 37 9.666435 0 - - 0 3 348 234 10.338870 0 - - 0 4 354 25 13.138028 0 - - 0 5 354 37 13.208847 0 - - 0 6 477 37 22.028063 0 - - 0 7 477 125 9.389512 0 - - 0 8 477 234 16.348776 0 - - 0 9 604 25 15.886898 0 - - 0 10 604 37 14.646552 0 - - 0 11 604 234 9.289545 0 - - 0 *45 PF01658 PF07994 94 11 113.848298 family 1, PF01658: Myo-inositol-1-phosphate synthase Comparison of INO1 gene sequences and products in Candida family 2, PF07994: Myo-inositol-1-phosphate synthase Comparison of INO1 gene sequences and products in Candida index pos1 pos2 score npdbs avgdist mindist nshort 0 24 96 9.238803 3 33.6149 32.8448 0 1 24 223 9.271063 3 22.1421 21.6306 0 2 24 289 9.582640 3 21.2450 20.8972 0 3 24 290 10.904607 3 21.8667 19.2798 0 4 24 303 11.716645 3 33.0190 32.6562 0 5 24 475 10.731429 3 20.8143 16.6859 0 6 24 476 11.639614 3 17.0491 14.4004 0 7 24 484 10.478243 3 23.2211 22.2343 0 8 24 489 10.446053 3 32.6408 31.2587 0 9 24 493 10.334404 3 36.7147 35.7996 0 10 156 166 9.504801 3 20.4711 15.8450 0 $46 PF02626 PF02682 89 13 113.180388 family 1, PF02626: Allophanate hydrolase subunit 2 family 2, PF02682: Allophanate hydrolase subunit 1 index pos1 pos2 score npdbs avgdist mindist nshort 0 489 548 14.331291 0 - - 0 1 489 582 27.296282 0 - - 0 2 489 666 11.025765 0 - - 0 3 489 673 14.048903 0 - - 0 4 496 582 13.093756 0 - - 0 5 499 582 20.049423 0 - - 0 6 501 340 15.459500 0 - - 0 7 501 548 14.977181 0 - - 0 8 501 582 26.445134 0 - - 0 9 501 666 11.436066 0 - - 0 10 501 673 14.768328 0 - - 0 11 526 582 10.282778 0 - - 0 12 527 673 9.321062 0 - - 0 #47 PF00203 PF00347 280 12 111.706677 family 1, PF00203: Ribosomal protein S19 family 2, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene index pos1 pos2 score npdbs avgdist mindist nshort 0 6 169 10.206371 0 - - 0 1 6 172 13.379129 0 - - 0 2 77 179 18.051760 0 - - 0 3 81 172 9.861553 0 - - 0 4 81 174 11.186753 0 - - 0 5 94 174 11.047761 0 - - 0 6 94 179 13.434780 0 - - 0 7 129 174 14.907958 0 - - 0 8 129 179 15.360429 0 - - 0 9 137 169 10.264824 0 - - 0 10 137 174 18.551104 0 - - 0 11 137 176 9.230985 0 - - 0 *48 PF00350 PF02212 69 18 110.448450 family 1, PF00350: Dynamin family Dynamin GTPase, a force-generating molecular switch. family 2, PF02212: Dynamin GTPase effector domain index pos1 pos2 score npdbs avgdist mindist nshort 0 18 17 9.142999 0 - - 0 1 18 68 16.085248 0 - - 0 2 21 17 9.149716 0 - - 0 3 39 17 14.352549 0 - - 0 4 39 39 9.605669 0 - - 0 5 39 68 19.168771 0 - - 0 6 45 68 13.241903 0 - - 0 7 295 17 9.784766 0 - - 0 8 295 68 17.934573 0 - - 0 9 323 17 12.762751 0 - - 0 10 323 39 12.359425 0 - - 0 11 329 17 10.697705 0 - - 0 12 329 68 16.045748 0 - - 0 13 330 17 10.808062 0 - - 0 14 330 68 17.382727 0 - - 0 15 521 39 9.207814 0 - - 0 16 539 68 10.611880 0 - - 0 17 572 68 9.653254 0 - - 0 $49 PF03524 PF04610 63 9 110.221247 family 1, PF03524: Conjugal transfer protein family 2, PF04610: TrbL/VirB6 plasmid conjugal transfer protein Essential components of the Ti plasmid trb system, a type index pos1 pos2 score npdbs avgdist mindist nshort 0 0 324 9.951672 0 - - 0 1 8 342 27.202074 0 - - 0 2 620 342 9.136319 0 - - 0 3 665 339 23.514423 0 - - 0 4 704 324 13.894548 0 - - 0 5 704 342 16.299276 0 - - 0 6 742 324 13.807819 0 - - 0 7 742 342 14.716071 0 - - 0 8 768 324 9.352996 0 - - 0 #50 PF00164 PF00318 313 10 109.559779 family 1, PF00164: Ribosomal protein S12 family 2, PF00318: Ribosomal protein S2 index pos1 pos2 score npdbs avgdist mindist nshort 0 111 189 9.945983 1 73.1720 73.1720 0 1 111 192 12.749703 1 69.0247 69.0247 0 2 111 267 12.080892 1 83.8572 83.8572 0 3 111 338 10.544416 1 70.3957 70.3957 0 4 140 358 9.967424 1 79.0217 79.0217 0 5 153 9 14.083482 1 96.5167 96.5167 0 6 166 9 13.868738 1 71.5374 71.5374 0 7 166 192 11.769355 1 54.8845 54.8845 0 8 166 378 15.077247 1 70.3381 70.3381 0 9 175 192 10.805942 1 51.6977 51.6977 0 $51 PF00809 PF02310 133 8 102.978315 family 1, PF00809: Pterin binding enzyme Crystal structure of the anti-bacterial sulfonamide drug family 2, PF02310: B12 binding domain How a protein prepares for B12 binding: structure and index pos1 pos2 score npdbs avgdist mindist nshort 0 6 9 9.232257 0 - - 0 1 6 14 9.382752 0 - - 0 2 6 32 10.426923 0 - - 0 3 6 33 9.489937 0 - - 0 4 8 14 11.330811 0 - - 0 5 407 46 21.516627 0 - - 0 6 454 46 27.706306 0 - - 0 7 541 46 18.712559 0 - - 0 *52 PF00984 PF03721 195 4 99.837574 family 1, PF00984: UDP-glucose/GDP-mannose dehydrogenase family, central domain Purification and characterization of guanosine family 2, PF03721: UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain Purification and characterization of guanosine index pos1 pos2 score npdbs avgdist mindist nshort 0 54 566 29.269998 1 9.6165 9.6165 1 1 60 101 23.674461 1 18.1368 18.1368 0 2 72 539 39.369920 1 16.3579 16.3579 0 3 72 540 13.217393 1 14.5997 14.5997 0 *53 PF03464 PF03465 98 11 99.510349 family 1, PF03464: eRF1 domain 2 The crystal structure of human eukaryotic release factor family 2, PF03465: eRF1 domain 3 The crystal structure of human eukaryotic release factor index pos1 pos2 score npdbs avgdist mindist nshort 0 8 144 10.588321 0 - - 0 1 62 144 12.603649 0 - - 0 2 62 165 11.975950 0 - - 0 3 62 167 9.550641 0 - - 0 4 64 144 13.240034 0 - - 0 5 64 165 9.597829 0 - - 0 6 126 174 9.416113 0 - - 0 7 174 143 9.946014 0 - - 0 8 174 167 9.259479 0 - - 0 9 184 149 13.155512 0 - - 0 10 184 174 13.010871 0 - - 0 54 PF00343 PF02666 94 9 96.089047 family 1, PF00343: Carbohydrate phosphorylase Control of phosphorylase b conformation by a modified family 2, PF02666: Phosphatidylserine decarboxylase Cloning, sequencing, and disruption of the Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 39 116 10.506258 0 - - 0 1 39 601 15.795325 0 - - 0 2 39 605 13.389062 0 - - 0 3 39 671 10.914961 0 - - 0 4 39 886 9.711913 0 - - 0 5 39 1055 10.339236 0 - - 0 6 1647 601 13.109290 0 - - 0 7 1647 605 10.106089 0 - - 0 8 1713 601 12.230347 0 - - 0 #55 PF00189 PF00410 308 11 95.926391 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein index pos1 pos2 score npdbs avgdist mindist nshort 0 10 214 13.109534 0 - - 0 1 10 274 10.478565 0 - - 0 2 101 10 10.065468 0 - - 0 3 101 260 10.408821 0 - - 0 4 101 262 13.079471 0 - - 0 5 102 71 10.522266 0 - - 0 6 102 260 10.431089 0 - - 0 7 114 262 9.837620 0 - - 0 8 123 346 10.004449 0 - - 0 9 132 260 9.271965 0 - - 0 10 132 262 11.490426 0 - - 0 #56 PF00318 PF00410 299 9 94.848197 family 1, PF00318: Ribosomal protein S2 family 2, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein index pos1 pos2 score npdbs avgdist mindist nshort 0 22 262 11.132666 0 - - 0 1 192 214 14.595032 0 - - 0 2 192 262 10.120126 0 - - 0 3 192 274 9.652548 0 - - 0 4 259 260 14.007299 0 - - 0 5 259 262 10.672578 0 - - 0 6 267 262 12.990218 0 - - 0 7 358 260 15.246586 0 - - 0 8 358 262 11.746453 0 - - 0 *57 PF00181 PF03947 456 8 94.773923 family 1, PF00181: Ribosomal Proteins L2, RNA binding domain family 2, PF03947: Ribosomal Proteins L2, C-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 9 19 24.015170 1 23.4880 23.4880 0 1 15 205 23.909351 1 13.8532 13.8532 0 2 31 205 27.726353 1 28.8047 28.8047 0 3 52 205 10.368699 1 8.6921 8.6921 1 4 55 174 17.049725 1 22.7508 22.7508 0 5 55 197 16.379393 1 19.3781 19.3781 0 6 107 205 18.125870 1 18.3225 18.3225 0 7 114 205 9.728755 1 20.6344 20.6344 0 *58 PF00120 PF03951 331 6 94.527501 family 1, PF00120: Glutamine synthetase, catalytic domain family 2, PF03951: Glutamine synthetase, beta-Grasp domain index pos1 pos2 score npdbs avgdist mindist nshort 0 174 128 14.162139 0 - - 0 1 178 93 13.869081 0 - - 0 2 183 90 34.919334 0 - - 0 3 536 93 11.612548 0 - - 0 4 542 93 9.407675 0 - - 0 5 606 93 18.487973 0 - - 0 *59 PF00046 PF00157 57 9 94.155986 family 1, PF00046: Homeobox domain The homeobox in perspective. family 2, PF00157: Pou domain - N-terminal to homeobox domain index pos1 pos2 score npdbs avgdist mindist nshort 0 24 33 16.439736 2 23.0894 21.1763 0 1 24 48 11.007039 2 30.0098 29.4495 0 2 24 54 12.199535 2 24.6509 21.0349 0 3 24 101 10.020630 2 19.6876 10.8650 0 4 24 109 11.229559 2 26.1161 21.8327 0 5 31 33 13.891988 2 27.7511 27.0184 0 6 31 48 9.537898 2 33.1635 32.0520 0 7 31 54 11.381720 2 28.4125 24.9818 0 8 40 54 24.612987 2 29.9308 27.9895 0 *60 PF02785 PF02786 266 5 91.752563 family 1, PF02785: Biotin carboxylase C-terminal domain Three-dimensional structure of the biotin carboxylase family 2, PF02786: Carbamoyl-phosphate synthase L chain, ATP binding domain Three-dimensional structure of the biotin carboxylase index pos1 pos2 score npdbs avgdist mindist nshort 0 106 269 26.208878 2 34.5322 33.8330 0 1 106 417 24.763799 2 21.6533 21.4742 0 2 106 494 11.067642 2 22.8479 22.3876 0 3 106 583 11.896301 2 8.4816 8.2783 2 4 106 590 17.815948 2 7.2532 7.0327 2 #61 PF00238 PF00347 281 9 91.705210 family 1, PF00238: Ribosomal protein L14p/L23e family 2, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene index pos1 pos2 score npdbs avgdist mindist nshort 0 0 174 13.093899 4 63.2907 48.6817 0 1 9 174 10.712668 4 66.8059 49.3157 0 2 91 179 9.297566 4 74.3851 57.6284 0 3 120 174 9.686948 4 67.3665 47.9836 0 4 253 169 10.164108 4 56.3054 39.0061 0 5 253 174 11.753168 4 59.6089 41.8305 0 6 259 174 10.018411 4 69.8195 52.7617 0 7 283 179 11.364522 4 54.0036 38.3444 0 8 315 174 11.592228 4 63.1233 46.3928 0 62 PF01964 PF02446 69 13 89.577807 family 1, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes family 2, PF02446: 4-alpha-glucanotransferase Disproportionating enzyme (4-alpha-glucanotransferase; EC index pos1 pos2 score npdbs avgdist mindist nshort 0 192 479 14.210528 0 - - 0 1 192 565 11.751085 0 - - 0 2 217 479 11.180298 0 - - 0 3 306 11 11.384268 0 - - 0 4 306 54 11.474449 0 - - 0 5 306 479 15.395457 0 - - 0 6 306 529 10.348795 0 - - 0 7 306 565 12.139720 0 - - 0 8 314 479 11.997625 0 - - 0 9 314 529 9.507296 0 - - 0 10 430 479 9.054031 0 - - 0 11 495 479 12.777008 0 - - 0 12 495 529 9.095322 0 - - 0 #63 PF00203 PF00673 287 12 86.703772 family 1, PF00203: Ribosomal protein S19 family 2, PF00673: ribosomal L5P family C-terminus index pos1 pos2 score npdbs avgdist mindist nshort 0 77 35 11.194250 0 - - 0 1 81 35 10.357215 0 - - 0 2 94 35 12.222936 0 - - 0 3 94 103 9.009283 0 - - 0 4 129 14 9.571800 0 - - 0 5 129 22 11.822580 0 - - 0 6 129 35 14.475773 0 - - 0 7 129 103 10.094291 0 - - 0 8 129 145 9.329830 0 - - 0 9 137 22 11.369013 0 - - 0 10 137 103 9.043787 0 - - 0 11 137 145 9.518484 0 - - 0 $64 PF01964 PF02401 115 9 86.364735 family 1, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes family 2, PF02401: LytB protein Identification of the Escherichia coli lytB gene, which is index pos1 pos2 score npdbs avgdist mindist nshort 0 306 142 17.137639 0 - - 0 1 306 171 13.509209 0 - - 0 2 306 453 14.980857 0 - - 0 3 323 10 14.221491 0 - - 0 4 323 130 9.962162 0 - - 0 5 323 142 12.365012 0 - - 0 6 323 171 11.936979 0 - - 0 7 492 6 9.786522 0 - - 0 8 495 142 10.322559 0 - - 0 *65 PF00140 PF04542 229 4 86.267809 family 1, PF00140: Sigma-70 factor, region 1.2 Crystal structure of a sigma 70 subunit fragment from E. family 2, PF04542: Sigma-70 region 2 Structure of the bacterial RNA polymerase promoter index pos1 pos2 score npdbs avgdist mindist nshort 0 3 130 11.288486 2 20.9578 19.7902 0 1 4 130 11.979602 2 24.7883 23.8466 0 2 16 121 19.018065 2 23.8413 22.8821 0 3 35 90 43.981658 2 3.5045 3.0026 2 #66 PF02574 PF02607 110 9 84.492623 family 1, PF02574: Homocysteine S-methyltransferase S-methylmethionine metabolism in Escherichia coli. family 2, PF02607: B12 binding domain How a protein binds B12: A 3.0 A X-ray structure of index pos1 pos2 score npdbs avgdist mindist nshort 0 102 51 13.319910 0 - - 0 1 102 77 11.412072 0 - - 0 2 102 80 18.441478 0 - - 0 3 322 74 9.302252 0 - - 0 4 329 80 14.139809 0 - - 0 5 439 51 10.053716 0 - - 0 6 439 77 10.364950 0 - - 0 7 439 80 14.537670 0 - - 0 8 613 80 9.191492 0 - - 0 67 PF02091 PF07991 97 8 83.513134 family 1, PF02091: Glycyl-tRNA synthetase alpha subunit family 2, PF07991: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid index pos1 pos2 score npdbs avgdist mindist nshort 0 45 18 9.464848 0 - - 0 1 45 98 10.319050 0 - - 0 2 45 118 10.753906 0 - - 0 3 45 147 10.324562 0 - - 0 4 45 166 9.257155 0 - - 0 5 45 177 11.280934 0 - - 0 6 45 208 10.209743 0 - - 0 7 45 227 11.902940 0 - - 0 #68 PF00189 PF00238 315 13 81.588732 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF00238: Ribosomal protein L14p/L23e index pos1 pos2 score npdbs avgdist mindist nshort 0 10 259 10.548650 0 - - 0 1 10 318 9.420363 0 - - 0 2 91 2 9.110154 0 - - 0 3 91 9 9.777959 0 - - 0 4 91 253 11.456667 0 - - 0 5 91 259 12.849513 0 - - 0 6 91 318 11.627534 0 - - 0 7 101 259 13.016690 0 - - 0 8 132 0 9.704211 0 - - 0 9 132 2 9.416860 0 - - 0 10 132 9 10.757007 0 - - 0 11 132 257 9.970928 0 - - 0 12 132 259 11.823267 0 - - 0 #69 PF00238 PF00410 312 8 80.702233 family 1, PF00238: Ribosomal protein L14p/L23e family 2, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein index pos1 pos2 score npdbs avgdist mindist nshort 0 0 260 11.087650 0 - - 0 1 253 260 12.376453 0 - - 0 2 253 346 9.415000 0 - - 0 3 257 260 9.220020 0 - - 0 4 259 260 12.823231 0 - - 0 5 259 262 12.495373 0 - - 0 6 315 260 10.350959 0 - - 0 7 318 262 9.057946 0 - - 0 #70 PF00177 PF00203 320 7 79.247883 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF00203: Ribosomal protein S19 index pos1 pos2 score npdbs avgdist mindist nshort 0 97 77 11.383859 1 70.4890 70.4890 0 1 97 94 10.648680 1 67.0176 67.0176 0 2 97 129 9.400765 1 60.2449 60.2449 0 3 300 77 14.508967 1 73.4748 73.4748 0 4 324 77 11.372118 1 76.7557 76.7557 0 5 358 77 9.606925 1 64.6420 64.6420 0 6 416 77 12.326575 1 78.0677 78.0677 0 71 PF00344 PF00410 255 7 76.364594 family 1, PF00344: eubacterial secY protein family 2, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein index pos1 pos2 score npdbs avgdist mindist nshort 0 11 214 12.010456 0 - - 0 1 38 214 16.531364 0 - - 0 2 38 260 11.185655 0 - - 0 3 38 262 9.085033 0 - - 0 4 389 262 9.644054 0 - - 0 5 856 214 11.635334 0 - - 0 6 1114 214 9.128613 0 - - 0 #72 PF00298 PF03947 262 5 75.922510 family 1, PF00298: Ribosomal protein L11, RNA binding domain High resolution solution structure of ribosomal protein family 2, PF03947: Ribosomal Proteins L2, C-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 0 197 15.269259 0 - - 0 1 0 207 22.140606 0 - - 0 2 45 19 16.467079 0 - - 0 3 92 259 16.677360 0 - - 0 4 120 207 16.326031 0 - - 0 #73 PF00177 PF00298 263 7 75.387673 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF00298: Ribosomal protein L11, RNA binding domain High resolution solution structure of ribosomal protein index pos1 pos2 score npdbs avgdist mindist nshort 0 304 0 15.868976 0 - - 0 1 304 92 14.988704 0 - - 0 2 323 45 11.753096 0 - - 0 3 324 45 15.456686 0 - - 0 4 324 92 14.095672 0 - - 0 5 343 120 9.591616 0 - - 0 6 344 92 14.081724 0 - - 0 74 PF00189 PF04565 293 7 72.885199 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF04565: RNA polymerase Rpb2, domain 3 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 10 9 11.017694 0 - - 0 1 10 49 10.464330 0 - - 0 2 101 9 13.224730 0 - - 0 3 101 49 11.671062 0 - - 0 4 121 9 9.554351 0 - - 0 5 123 9 16.176162 0 - - 0 6 132 9 11.935709 0 - - 0 #75 PF00189 PF00281 287 8 72.684155 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF00281: Ribosomal protein L5 index pos1 pos2 score npdbs avgdist mindist nshort 0 10 84 10.613794 0 - - 0 1 91 7 12.069657 0 - - 0 2 91 84 10.199779 0 - - 0 3 101 7 10.361422 0 - - 0 4 101 19 9.263330 0 - - 0 5 102 54 9.703939 0 - - 0 6 102 84 9.682858 0 - - 0 7 132 7 9.802225 0 - - 0 76 PF01493 PF01964 112 10 70.363930 family 1, PF01493: GXGXG motif The formylmethanofuran dehydrogenase isoenzymes in family 2, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes index pos1 pos2 score npdbs avgdist mindist nshort 0 15 541 9.490520 0 - - 0 1 131 478 9.635744 0 - - 0 2 131 541 13.523620 0 - - 0 3 135 20 10.536867 0 - - 0 4 279 541 10.981483 0 - - 0 5 448 20 12.455728 0 - - 0 6 448 185 9.196848 0 - - 0 7 448 240 10.391886 0 - - 0 8 448 478 9.564177 0 - - 0 9 448 519 9.690877 0 - - 0 #77 PF00163 PF00687 242 6 69.698220 family 1, PF00163: Ribosomal protein S4/S9 N-terminal domain The crystal structure of ribosomal protein S4 reveals a family 2, PF00687: Ribosomal protein L1p/L10e family index pos1 pos2 score npdbs avgdist mindist nshort 0 56 547 10.222376 0 - - 0 1 108 547 14.970773 0 - - 0 2 118 547 10.604397 0 - - 0 3 132 366 9.444599 0 - - 0 4 132 382 12.523708 0 - - 0 5 132 547 21.687082 0 - - 0 78 PF01641 PF02347 127 5 67.518825 family 1, PF01641: SelR domain Novel selenoproteins identified in silico and in vivo by family 2, PF02347: Glycine cleavage system P-protein Genetics of the synthesis of serine from glycine and the index pos1 pos2 score npdbs avgdist mindist nshort 0 64 5 15.117766 0 - - 0 1 64 237 10.927109 0 - - 0 2 64 293 13.541024 0 - - 0 3 64 316 15.437057 0 - - 0 4 64 318 12.495872 0 - - 0 *79 PF01232 PF08125 87 8 67.242724 family 1, PF01232: Mannitol dehydrogenase Rossmann domain family 2, PF08125: Mannitol dehydrogenase C-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 11 9 9.591824 1 12.1710 12.1710 0 1 11 134 10.004154 1 18.9792 18.9792 0 2 11 138 17.655995 1 19.2457 19.2457 0 3 42 138 9.456871 1 25.9587 25.9587 0 4 77 134 9.678722 1 32.1696 32.1696 0 5 77 138 13.078994 1 32.4162 32.4162 0 6 163 138 10.274321 1 14.9978 14.9978 0 7 164 138 10.636587 1 10.9015 10.9015 0 #80 PF00164 PF00411 315 7 66.719949 family 1, PF00164: Ribosomal protein S12 family 2, PF00411: Ribosomal protein S11 index pos1 pos2 score npdbs avgdist mindist nshort 0 111 99 9.537401 1 78.7040 78.7040 0 1 165 99 10.325831 1 80.6090 80.6090 0 2 166 40 13.267869 1 73.4578 73.4578 0 3 166 99 11.816589 1 71.8184 71.8184 0 4 166 145 12.313210 1 61.5834 61.5834 0 5 175 38 9.208177 1 74.1531 74.1531 0 6 175 99 10.250922 1 69.7645 69.7645 0 81 PF02554 PF02652 57 8 66.428667 family 1, PF02554: Carbon starvation protein CstA Molecular and functional characterization of a carbon family 2, PF02652: L-lactate permease Three overlapping lct genes involved in L-lactate index pos1 pos2 score npdbs avgdist mindist nshort 0 19 134 10.818302 0 - - 0 1 54 1063 11.034378 0 - - 0 2 61 1063 11.079467 0 - - 0 3 83 1063 20.272102 0 - - 0 4 127 1063 20.397146 0 - - 0 5 618 1063 12.384703 0 - - 0 6 649 134 16.992745 0 - - 0 7 649 1063 24.996430 0 - - 0 *82 PF00189 PF07650 320 5 64.066211 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF07650: KH domain Conserved structures and diversity of functions of index pos1 pos2 score npdbs avgdist mindist nshort 0 91 15 9.954601 1 29.4458 29.4458 0 1 91 16 11.334673 1 31.8073 31.8073 0 2 91 104 12.147575 1 15.2518 15.2518 0 3 101 16 9.790019 1 32.5745 32.5745 0 4 132 15 17.996094 1 21.9735 21.9735 0 #83 PF00177 PF00189 311 14 63.058062 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of index pos1 pos2 score npdbs avgdist mindist nshort 0 25 10 9.050208 1 81.1991 81.1991 0 1 25 91 11.097642 1 66.5507 66.5507 0 2 97 10 10.933027 1 82.9383 82.9383 0 3 97 91 12.722331 1 68.7669 68.7669 0 4 300 10 9.291138 1 69.8704 69.8704 0 5 300 91 9.935712 1 55.6169 55.6169 0 6 300 132 9.054435 1 53.6532 53.6532 0 7 304 10 9.657496 1 62.9405 62.9405 0 8 304 91 12.209463 1 49.1406 49.1406 0 9 304 132 10.656257 1 48.7631 48.7631 0 10 324 10 9.262656 1 74.7054 74.7054 0 11 324 91 13.551295 1 60.2949 60.2949 0 12 324 101 9.541504 1 55.5473 55.5473 0 13 324 132 10.373359 1 58.0241 58.0241 0 84 PF01293 PF02503 46 8 62.737819 family 1, PF01293: Phosphoenolpyruvate carboxykinase Snapshot of an enzyme reaction intermediate in the family 2, PF02503: Polyphosphate kinase Transcription of ppk from Acinetobacter sp. strain ADP1, index pos1 pos2 score npdbs avgdist mindist nshort 0 94 609 10.151949 0 - - 0 1 94 745 10.603302 0 - - 0 2 100 110 10.632247 0 - - 0 3 179 109 18.152717 0 - - 0 4 179 408 11.683220 0 - - 0 5 179 572 9.183876 0 - - 0 6 179 599 13.494019 0 - - 0 7 179 663 9.355948 0 - - 0 85 PF00471 PF01964 109 8 62.591576 family 1, PF00471: Ribosomal protein L33 family 2, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes index pos1 pos2 score npdbs avgdist mindist nshort 0 7 306 9.343898 0 - - 0 1 10 306 10.865337 0 - - 0 2 53 306 23.942080 0 - - 0 3 53 314 14.532291 0 - - 0 4 53 406 9.176136 0 - - 0 5 53 430 10.598123 0 - - 0 6 53 495 19.126814 0 - - 0 7 68 306 11.429505 0 - - 0 *86 PF03463 PF03465 93 6 62.013158 family 1, PF03463: eRF1 domain 1 The crystal structure of human eukaryotic release factor family 2, PF03465: eRF1 domain 3 The crystal structure of human eukaryotic release factor index pos1 pos2 score npdbs avgdist mindist nshort 0 173 4 10.889157 0 - - 0 1 173 165 11.009534 0 - - 0 2 173 167 10.725867 0 - - 0 3 173 174 9.991443 0 - - 0 4 186 174 9.077800 0 - - 0 5 247 29 9.201410 0 - - 0 #87 PF00731 PF01175 77 7 61.865730 family 1, PF00731: AIR carboxylase Crystal structure of Escherichia coli PurE, an unusual family 2, PF01175: Urocanase index pos1 pos2 score npdbs avgdist mindist nshort 0 141 75 9.325961 0 - - 0 1 141 103 9.292461 0 - - 0 2 141 264 9.531586 0 - - 0 3 141 291 9.579341 0 - - 0 4 141 685 12.089130 0 - - 0 5 164 820 13.614640 0 - - 0 6 204 820 13.324775 0 - - 0 *88 PF04560 PF04565 384 6 60.743347 family 1, PF04560: RNA polymerase Rpb2, domain 7 Structural basis of transcription: RNA polymerase II at 2.8 family 2, PF04565: RNA polymerase Rpb2, domain 3 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 32 71 13.714457 2 44.2336 39.6863 0 1 66 10 14.973100 2 59.0368 44.6659 0 2 66 43 9.349903 2 54.9450 45.4468 0 3 207 28 14.967430 2 43.4598 38.1941 0 4 207 30 14.586335 2 42.6923 39.4621 0 5 207 43 16.532008 2 48.7775 44.0358 0 89 PF00410 PF04565 288 7 60.611155 family 1, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein family 2, PF04565: RNA polymerase Rpb2, domain 3 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 214 12 11.485791 0 - - 0 1 214 16 9.078802 0 - - 0 2 260 9 13.948315 0 - - 0 3 260 49 10.762239 0 - - 0 4 262 9 13.450115 0 - - 0 5 262 49 10.200509 0 - - 0 6 346 9 9.409777 0 - - 0 90 PF00670 PF01964 83 8 60.185524 family 1, PF00670: S-adenosyl-L-homocysteine hydrolase, NAD binding domain family 2, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes index pos1 pos2 score npdbs avgdist mindist nshort 0 5 306 12.129753 0 - - 0 1 66 176 9.367009 0 - - 0 2 66 306 22.708337 0 - - 0 3 66 314 13.579005 0 - - 0 4 66 323 17.641022 0 - - 0 5 66 430 10.401474 0 - - 0 6 80 306 9.591029 0 - - 0 7 216 306 9.480944 0 - - 0 #91 PF00177 PF00238 302 7 59.918917 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF00238: Ribosomal protein L14p/L23e index pos1 pos2 score npdbs avgdist mindist nshort 0 25 259 11.836421 0 - - 0 1 25 318 9.947379 0 - - 0 2 97 259 13.997146 0 - - 0 3 97 318 10.264497 0 - - 0 4 300 259 11.940847 0 - - 0 5 300 318 10.313186 0 - - 0 6 324 259 10.438147 0 - - 0 92 PF01642 PF03308 52 5 58.626583 family 1, PF01642: Methylmalonyl-CoA mutase How coenzyme B12 radicals are generated: the crystal family 2, PF03308: ArgK protein Phosphorylation of the periplasmic binding protein in two index pos1 pos2 score npdbs avgdist mindist nshort 0 92 153 12.110643 0 - - 0 1 600 291 13.895424 0 - - 0 2 616 244 9.872954 0 - - 0 3 667 291 9.237543 0 - - 0 4 753 289 14.938475 0 - - 0 93 PF01964 PF02572 79 5 58.121841 family 1, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes family 2, PF02572: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP Cobalamin (vitamin B12) biosynthesis: identification and index pos1 pos2 score npdbs avgdist mindist nshort 0 136 162 13.044259 0 - - 0 1 157 162 10.955005 0 - - 0 2 185 162 11.549994 0 - - 0 3 367 159 9.145820 0 - - 0 4 519 162 13.426769 0 - - 0 #94 PF02538 PF05378 72 4 56.570280 family 1, PF02538: Hydantoinase B/oxoprolinase Cloning and sequencing of the genes involved in the family 2, PF05378: Hydantoinase/oxoprolinase N-terminal region index pos1 pos2 score npdbs avgdist mindist nshort 0 26 123 10.708768 0 - - 0 1 79 123 17.634513 0 - - 0 2 678 191 11.390347 0 - - 0 3 927 123 16.836653 0 - - 0 *95 PF00152 PF01336 254 4 55.943803 family 1, PF00152: tRNA synthetases class II (D, K and N) family 2, PF01336: OB-fold nucleic acid binding domain Class II aminoacyl transfer RNA synthetases: crystal index pos1 pos2 score npdbs avgdist mindist nshort 0 12 244 22.352473 5 25.3501 22.6419 0 1 75 244 11.124224 5 47.7544 36.8269 0 2 239 244 9.002071 5 44.4240 36.8269 0 3 269 244 13.465039 5 45.2534 41.9778 0 *96 PF00009 PF00679 336 2 55.358642 family 1, PF00009: Elongation factor Tu GTP binding domain Visualization of elongation factor Tu on the Escherichia family 2, PF00679: Elongation factor G C-terminus index pos1 pos2 score npdbs avgdist mindist nshort 0 481 401 26.682288 1 26.6954 26.6954 0 1 483 401 28.676356 1 17.9991 17.9991 0 #97 PF00163 PF00673 249 6 54.502379 family 1, PF00163: Ribosomal protein S4/S9 N-terminal domain The crystal structure of ribosomal protein S4 reveals a family 2, PF00673: ribosomal L5P family C-terminus index pos1 pos2 score npdbs avgdist mindist nshort 0 108 118 9.860946 0 - - 0 1 132 22 12.581312 0 - - 0 2 132 103 10.857756 0 - - 0 3 132 118 19.112237 0 - - 0 4 132 144 9.533292 0 - - 0 5 132 145 10.686897 0 - - 0 98 PF01964 PF05221 83 5 52.237763 family 1, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes family 2, PF05221: S-adenosyl-L-homocysteine hydrolase index pos1 pos2 score npdbs avgdist mindist nshort 0 136 303 9.033501 0 - - 0 1 192 303 18.181006 0 - - 0 2 306 106 14.030462 0 - - 0 3 306 603 10.573085 0 - - 0 4 323 306 10.850083 0 - - 0 $99 PF01964 PF02607 93 4 52.169155 family 1, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes family 2, PF02607: B12 binding domain How a protein binds B12: A 3.0 A X-ray structure of index pos1 pos2 score npdbs avgdist mindist nshort 0 192 30 14.354698 0 - - 0 1 217 30 11.979761 0 - - 0 2 306 30 13.528318 0 - - 0 3 323 30 12.306381 0 - - 0 100 PF01274 PF01293 58 5 52.013524 family 1, PF01274: Malate synthase Crystal structure of Escherichia coli malate synthase G family 2, PF01293: Phosphoenolpyruvate carboxykinase Snapshot of an enzyme reaction intermediate in the index pos1 pos2 score npdbs avgdist mindist nshort 0 489 496 9.121131 0 - - 0 1 494 496 10.747362 0 - - 0 2 497 496 11.272332 0 - - 0 3 722 496 9.054651 0 - - 0 4 726 496 11.818054 0 - - 0 #101 PF01440 PF08283 74 4 51.867501 family 1, PF01440: Geminivirus AL2 protein Transactivation in a geminivirus: AL2 gene product is family 2, PF08283: Geminivirus rep protein central domain The structure of a replication initiator unites diverse index pos1 pos2 score npdbs avgdist mindist nshort 0 15 82 12.415948 0 - - 0 1 15 83 17.180502 0 - - 0 2 160 82 28.815736 0 - - 0 3 160 83 33.178882 0 - - 0 102 PF00330 PF02572 86 4 49.980266 family 1, PF00330: Aconitase family (aconitate hydratase) family 2, PF02572: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP Cobalamin (vitamin B12) biosynthesis: identification and index pos1 pos2 score npdbs avgdist mindist nshort 0 666 162 14.674029 0 - - 0 1 1195 162 10.160146 0 - - 0 2 2030 162 14.124619 0 - - 0 3 2047 162 11.021474 0 - - 0 #103 PF00281 PF00410 281 6 49.823098 family 1, PF00281: Ribosomal protein L5 family 2, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein index pos1 pos2 score npdbs avgdist mindist nshort 0 7 214 13.548883 0 - - 0 1 7 260 11.112627 0 - - 0 2 7 262 10.227699 0 - - 0 3 19 260 11.792623 0 - - 0 4 19 262 11.118412 0 - - 0 5 54 214 9.057882 0 - - 0 *104 PF01450 PF07991 174 5 49.784459 family 1, PF01450: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid family 2, PF07991: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid index pos1 pos2 score npdbs avgdist mindist nshort 0 14 229 10.981308 2 24.5538 22.9773 0 1 18 161 10.122309 2 29.1385 27.4054 0 2 18 227 9.144043 2 31.0619 29.9937 0 3 206 177 11.312397 2 8.8995 7.4031 1 4 216 177 10.039956 2 6.2223 3.5298 2 *105 PF04997 PF05000 324 5 49.575137 family 1, PF04997: RNA polymerase Rpb1, domain 1 Structural modules of the large subunits of RNA polymerase. family 2, PF05000: RNA polymerase Rpb1, domain 4 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 214 19 9.922263 2 74.5964 71.9396 0 1 227 19 14.904564 2 63.4094 61.1757 0 2 227 105 9.008127 2 65.4493 60.2778 0 3 1557 19 9.823998 2 77.0677 70.0368 0 4 1949 19 9.685951 2 69.8878 65.6210 0 #106 PF00809 PF02607 112 4 48.487970 family 1, PF00809: Pterin binding enzyme Crystal structure of the anti-bacterial sulfonamide drug family 2, PF02607: B12 binding domain How a protein binds B12: A 3.0 A X-ray structure of index pos1 pos2 score npdbs avgdist mindist nshort 0 367 80 11.665311 0 - - 0 1 407 80 10.131242 0 - - 0 2 454 80 13.544555 0 - - 0 3 532 80 13.146866 0 - - 0 $107 PF00738 PF05094 79 6 47.730843 family 1, PF00738: Polyhedrin family 2, PF05094: Late expression factor 9 (LEF-9) Characterization of late gene expression factors lef-9 and index pos1 pos2 score npdbs avgdist mindist nshort 0 158 227 11.354859 0 - - 0 1 168 227 9.768443 0 - - 0 2 170 238 9.608127 0 - - 0 3 170 284 10.258348 0 - - 0 4 174 238 9.400065 0 - - 0 5 174 284 10.664844 0 - - 0 108 PF00670 PF00793 86 6 47.331218 family 1, PF00670: S-adenosyl-L-homocysteine hydrolase, NAD binding domain family 2, PF00793: DAHP synthetase I family Crystal structure of phenylalanine-regulated index pos1 pos2 score npdbs avgdist mindist nshort 0 4 182 9.692914 0 - - 0 1 5 289 9.481745 0 - - 0 2 66 222 10.309319 0 - - 0 3 66 289 18.613889 0 - - 0 4 66 305 12.972509 0 - - 0 5 267 289 10.494149 0 - - 0 *109 PF00140 PF04539 225 3 47.313162 family 1, PF00140: Sigma-70 factor, region 1.2 Crystal structure of a sigma 70 subunit fragment from E. family 2, PF04539: Sigma-70 region 3 Structure of the bacterial RNA polymerase promoter index pos1 pos2 score npdbs avgdist mindist nshort 0 16 9 14.503701 1 38.0388 38.0388 0 1 16 86 9.189969 1 53.6680 53.6680 0 2 35 66 23.619492 1 40.4083 40.4083 0 #110 PF00189 PF00347 280 5 46.773106 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene index pos1 pos2 score npdbs avgdist mindist nshort 0 10 179 11.964676 0 - - 0 1 101 174 9.708332 0 - - 0 2 102 174 9.907571 0 - - 0 3 132 172 9.257464 0 - - 0 4 132 174 12.266508 0 - - 0 #111 PF01968 PF02538 72 4 45.696676 family 1, PF01968: Hydantoinase/oxoprolinase The amino acid sequence of rat kidney 5-oxo-L-prolinase family 2, PF02538: Hydantoinase B/oxoprolinase Cloning and sequencing of the genes involved in the index pos1 pos2 score npdbs avgdist mindist nshort 0 145 678 14.778647 0 - - 0 1 152 265 9.253422 0 - - 0 2 152 596 11.573648 0 - - 0 3 197 678 13.047821 0 - - 0 112 PF01293 PF02153 63 4 44.654293 family 1, PF01293: Phosphoenolpyruvate carboxykinase Snapshot of an enzyme reaction intermediate in the family 2, PF02153: Prephenate dehydrogenase index pos1 pos2 score npdbs avgdist mindist nshort 0 179 246 12.621367 0 - - 0 1 179 251 9.121220 0 - - 0 2 179 489 12.574443 0 - - 0 3 179 592 10.337264 0 - - 0 113 PF00793 PF05221 85 4 44.640730 family 1, PF00793: DAHP synthetase I family Crystal structure of phenylalanine-regulated family 2, PF05221: S-adenosyl-L-homocysteine hydrolase index pos1 pos2 score npdbs avgdist mindist nshort 0 289 101 10.605687 0 - - 0 1 289 106 11.699286 0 - - 0 2 289 306 10.009130 0 - - 0 3 289 307 12.326631 0 - - 0 #114 PF00410 PF03947 313 5 44.205072 family 1, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein family 2, PF03947: Ribosomal Proteins L2, C-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 214 204 11.620608 0 - - 0 1 262 19 10.711895 0 - - 0 2 262 197 10.406058 0 - - 0 3 262 207 14.144109 0 - - 0 4 262 258 9.696420 0 - - 0 #115 PF04560 PF05000 274 4 43.685802 family 1, PF04560: RNA polymerase Rpb2, domain 7 Structural basis of transcription: RNA polymerase II at 2.8 family 2, PF05000: RNA polymerase Rpb1, domain 4 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 12 19 10.268935 2 43.5624 41.1542 0 1 29 19 9.620338 2 60.6798 59.3979 0 2 32 19 13.398682 2 61.8364 55.8390 0 3 152 19 10.397850 2 75.4366 71.2030 0 *116 PF00217 PF02807 158 8 43.332200 family 1, PF00217: ATP:guanido phosphotransferase, C-terminal catalytic domain Structure of mitochondrial creatine kinase. family 2, PF02807: ATP:guanido phosphotransferase, N-terminal domain Structure of mitochondrial creatine kinase. index pos1 pos2 score npdbs avgdist mindist nshort 0 42 63 11.218386 4 18.2559 18.1712 0 1 42 90 9.522727 4 19.9881 19.4026 0 2 43 56 9.596794 4 22.8061 19.9840 0 3 43 57 13.428350 4 25.5995 23.7024 0 4 43 63 16.084801 4 20.9006 20.7196 0 5 43 90 17.184503 4 22.2195 21.6133 0 6 137 63 10.982796 4 12.1208 10.9371 0 7 137 90 11.119830 4 14.5030 12.6093 0 #117 PF00203 PF00416 295 4 43.225278 family 1, PF00203: Ribosomal protein S19 family 2, PF00416: Ribosomal protein S13/S18 index pos1 pos2 score npdbs avgdist mindist nshort 0 6 215 10.954058 1 33.0276 33.0276 0 1 129 215 12.797053 1 24.1606 24.1606 0 2 137 183 12.197185 1 5.5069 5.5069 1 3 137 215 11.804060 1 18.6581 18.6581 0 #118 PF00177 PF00281 284 4 42.285646 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF00281: Ribosomal protein L5 index pos1 pos2 score npdbs avgdist mindist nshort 0 25 7 12.868050 0 - - 0 1 304 7 12.228083 0 - - 0 2 304 84 9.130932 0 - - 0 3 343 7 9.978949 0 - - 0 #119 PF00623 PF04560 275 3 42.196489 family 1, PF00623: RNA polymerase Rpb1, domain 2 Structural modules of the large subunits of RNA polymerase. family 2, PF04560: RNA polymerase Rpb2, domain 7 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 52 66 23.388967 2 28.8074 17.3537 0 1 387 12 9.074462 2 15.9579 15.7046 0 2 455 207 9.733060 2 39.9460 37.9296 0 120 PF00152 PF05000 244 4 42.155417 family 1, PF00152: tRNA synthetases class II (D, K and N) family 2, PF05000: RNA polymerase Rpb1, domain 4 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 263 19 10.314037 0 - - 0 1 298 19 10.165262 0 - - 0 2 856 19 10.752627 0 - - 0 3 1081 19 10.923495 0 - - 0 121 PF00464 PF01175 77 4 42.116830 family 1, PF00464: Serine hydroxymethyltransferase family 2, PF01175: Urocanase index pos1 pos2 score npdbs avgdist mindist nshort 0 72 571 9.552950 0 - - 0 1 912 131 12.215020 0 - - 0 2 912 571 14.115283 0 - - 0 3 912 670 13.626137 0 - - 0 122 PF00490 PF03116 51 5 41.611909 family 1, PF00490: Delta-aminolevulinic acid dehydratase family 2, PF03116: NQR2, RnfD, RnfE family Effects of changes in membrane sodium flux on virulence index pos1 pos2 score npdbs avgdist mindist nshort 0 143 502 10.976102 0 - - 0 1 151 502 10.976102 0 - - 0 2 381 414 9.197418 0 - - 0 3 387 207 10.718825 0 - - 0 4 387 414 12.965741 0 - - 0 #123 PF00203 PF00410 322 5 41.416744 family 1, PF00203: Ribosomal protein S19 family 2, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein index pos1 pos2 score npdbs avgdist mindist nshort 0 77 262 9.443669 0 - - 0 1 94 260 9.084384 0 - - 0 2 94 262 9.473749 0 - - 0 3 129 260 15.605655 0 - - 0 4 129 262 9.898623 0 - - 0 #124 PF00347 PF03947 286 4 41.336636 family 1, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene family 2, PF03947: Ribosomal Proteins L2, C-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 172 207 12.430531 2 113.8299 101.1055 0 1 174 204 10.322396 2 115.8655 102.1322 0 2 174 207 11.162694 2 119.2976 105.3718 0 3 176 207 9.714447 2 119.2377 106.2195 0 125 PF00344 PF00673 256 4 41.125924 family 1, PF00344: eubacterial secY protein family 2, PF00673: ribosomal L5P family C-terminus index pos1 pos2 score npdbs avgdist mindist nshort 0 38 35 11.208587 0 - - 0 1 211 35 10.192578 0 - - 0 2 852 35 10.328927 0 - - 0 3 856 35 9.395836 0 - - 0 #126 PF00411 PF03947 313 4 40.559665 family 1, PF00411: Ribosomal protein S11 family 2, PF03947: Ribosomal Proteins L2, C-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 38 197 9.153391 0 - - 0 1 38 207 11.016204 0 - - 0 2 40 197 11.383782 0 - - 0 3 99 197 9.006293 0 - - 0 127 PF00285 PF00521 193 3 40.272397 family 1, PF00285: Citrate synthase family 2, PF00521: DNA gyrase/topoisomerase IV, subunit A index pos1 pos2 score npdbs avgdist mindist nshort 0 750 80 15.595800 0 - - 0 1 750 85 12.357908 0 - - 0 2 750 114 12.318692 0 - - 0 #128 PF00164 PF00298 262 3 40.099596 family 1, PF00164: Ribosomal protein S12 family 2, PF00298: Ribosomal protein L11, RNA binding domain High resolution solution structure of ribosomal protein index pos1 pos2 score npdbs avgdist mindist nshort 0 111 92 16.471588 0 - - 0 1 113 92 10.016953 0 - - 0 2 165 0 13.611058 0 - - 0 129 PF00330 PF01964 126 7 39.257149 family 1, PF00330: Aconitase family (aconitate hydratase) family 2, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes index pos1 pos2 score npdbs avgdist mindist nshort 0 629 323 10.077400 0 - - 0 1 639 323 13.226440 0 - - 0 2 755 274 10.731807 0 - - 0 3 755 427 9.947757 0 - - 0 4 755 437 9.815957 0 - - 0 5 755 444 9.731561 0 - - 0 6 2036 323 10.199303 0 - - 0 130 PF00347 PF04565 257 4 39.101064 family 1, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene family 2, PF04565: RNA polymerase Rpb2, domain 3 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 172 9 13.022661 0 - - 0 1 179 16 9.267619 0 - - 0 2 179 29 9.668176 0 - - 0 3 179 49 11.870365 0 - - 0 131 PF00478 PF01175 79 4 38.710016 family 1, PF00478: IMP dehydrogenase / GMP reductase domain Crystal structure of Tritrichomonas foetus family 2, PF01175: Urocanase index pos1 pos2 score npdbs avgdist mindist nshort 0 19 820 9.716705 0 - - 0 1 466 820 9.027927 0 - - 0 2 567 820 10.040509 0 - - 0 3 620 820 9.924877 0 - - 0 #132 PF00164 PF00238 320 4 38.626148 family 1, PF00164: Ribosomal protein S12 family 2, PF00238: Ribosomal protein L14p/L23e index pos1 pos2 score npdbs avgdist mindist nshort 0 140 259 12.313756 0 - - 0 1 204 253 9.433845 0 - - 0 2 206 283 9.140631 0 - - 0 3 206 315 10.033464 0 - - 0 #133 PF04561 PF04566 172 2 38.266265 family 1, PF04561: RNA polymerase Rpb2, domain 2 Structural basis of transcription: RNA polymerase II at 2.8 family 2, PF04566: RNA polymerase Rpb2, domain 4 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 226 6 15.734259 1 11.9678 11.9678 0 1 232 52 22.532007 1 40.7576 40.7576 0 134 PF01175 PF03949 75 3 38.187470 family 1, PF01175: Urocanase family 2, PF03949: Malic enzyme, NAD binding domain index pos1 pos2 score npdbs avgdist mindist nshort 0 820 160 12.388472 0 - - 0 1 820 370 15.462529 0 - - 0 2 820 375 10.336470 0 - - 0 $135 PF02534 PF04610 50 3 38.048707 family 1, PF02534: TraG/TraD family Sequence and analysis of the 60 kb conjugative, family 2, PF04610: TrbL/VirB6 plasmid conjugal transfer protein Essential components of the Ti plasmid trb system, a type index pos1 pos2 score npdbs avgdist mindist nshort 0 944 324 13.578293 0 - - 0 1 944 342 15.268791 0 - - 0 2 1056 339 9.201624 0 - - 0 #136 PF00163 PF00238 276 6 37.615572 family 1, PF00163: Ribosomal protein S4/S9 N-terminal domain The crystal structure of ribosomal protein S4 reveals a family 2, PF00238: Ribosomal protein L14p/L23e index pos1 pos2 score npdbs avgdist mindist nshort 0 56 120 9.325082 0 - - 0 1 108 120 9.517544 0 - - 0 2 132 0 10.171052 0 - - 0 3 132 9 10.330903 0 - - 0 4 132 253 10.662184 0 - - 0 5 132 318 13.364062 0 - - 0 #137 PF00410 PF00416 283 3 37.356524 family 1, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein family 2, PF00416: Ribosomal protein S13/S18 index pos1 pos2 score npdbs avgdist mindist nshort 0 214 15 10.749281 0 - - 0 1 214 215 15.565934 0 - - 0 2 262 215 9.845166 0 - - 0 #138 PF00189 PF00203 332 4 37.349002 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF00203: Ribosomal protein S19 index pos1 pos2 score npdbs avgdist mindist nshort 0 10 77 12.037112 1 54.7696 54.7696 0 1 121 129 9.483417 1 57.0867 57.0867 0 2 132 81 9.398193 1 58.4552 58.4552 0 3 132 94 9.240821 1 59.3914 59.3914 0 139 PF00189 PF00344 263 4 36.321279 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF00344: eubacterial secY protein index pos1 pos2 score npdbs avgdist mindist nshort 0 101 852 11.351495 0 - - 0 1 132 38 11.449231 0 - - 0 2 132 852 10.209303 0 - - 0 3 132 856 10.816264 0 - - 0 140 PF01175 PF01808 78 3 36.102564 family 1, PF01175: Urocanase family 2, PF01808: AICARFT/IMPCHase bienzyme Molecular cloning and expression of a rat cDNA encoding 5- index pos1 pos2 score npdbs avgdist mindist nshort 0 820 265 11.792599 0 - - 0 1 820 303 10.308475 0 - - 0 2 820 459 14.001493 0 - - 0 141 PF00318 PF00623 236 3 35.711976 family 1, PF00318: Ribosomal protein S2 family 2, PF00623: RNA polymerase Rpb1, domain 2 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 22 52 14.917517 0 - - 0 1 118 52 10.710539 0 - - 0 2 130 395 10.083923 0 - - 0 #142 PF00177 PF00181 395 3 35.178970 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF00181: Ribosomal Proteins L2, RNA binding domain index pos1 pos2 score npdbs avgdist mindist nshort 0 62 24 13.066726 0 - - 0 1 62 55 11.410829 0 - - 0 2 343 73 10.701420 0 - - 0 #143 PF00164 PF00181 404 3 35.023075 family 1, PF00164: Ribosomal protein S12 family 2, PF00181: Ribosomal Proteins L2, RNA binding domain index pos1 pos2 score npdbs avgdist mindist nshort 0 140 24 16.041461 0 - - 0 1 140 73 9.847466 0 - - 0 2 175 15 9.134151 0 - - 0 #144 PF00163 PF00347 240 3 34.720253 family 1, PF00163: Ribosomal protein S4/S9 N-terminal domain The crystal structure of ribosomal protein S4 reveals a family 2, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene index pos1 pos2 score npdbs avgdist mindist nshort 0 102 179 11.318867 0 - - 0 1 108 179 10.258455 0 - - 0 2 132 179 13.142934 0 - - 0 #145 PF00410 PF00673 287 3 34.019228 family 1, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein family 2, PF00673: ribosomal L5P family C-terminus index pos1 pos2 score npdbs avgdist mindist nshort 0 214 14 12.323724 0 - - 0 1 214 35 11.697111 0 - - 0 2 260 35 11.106474 0 - - 0 146 PF00281 PF00344 257 3 33.927454 family 1, PF00281: Ribosomal protein L5 family 2, PF00344: eubacterial secY protein index pos1 pos2 score npdbs avgdist mindist nshort 0 7 38 10.891489 0 - - 0 1 7 389 11.496424 0 - - 0 2 7 852 11.539542 0 - - 0 147 PF00298 PF04997 236 3 33.816388 family 1, PF00298: Ribosomal protein L11, RNA binding domain High resolution solution structure of ribosomal protein family 2, PF04997: RNA polymerase Rpb1, domain 1 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 0 106 11.565246 0 - - 0 1 0 1529 11.377654 0 - - 0 2 0 1903 10.873489 0 - - 0 #148 PF00347 PF00416 276 3 33.450974 family 1, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene family 2, PF00416: Ribosomal protein S13/S18 index pos1 pos2 score npdbs avgdist mindist nshort 0 174 162 10.321784 0 - - 0 1 174 215 12.143162 0 - - 0 2 179 15 10.986031 0 - - 0 149 PF00318 PF00448 226 3 33.278921 family 1, PF00318: Ribosomal protein S2 family 2, PF00448: SRP54-type protein, GTPase domain Crystal structure of the NG domain from the index pos1 pos2 score npdbs avgdist mindist nshort 0 22 246 13.018840 0 - - 0 1 192 246 9.141076 0 - - 0 2 358 246 11.119007 0 - - 0 $150 PF01407 PF08283 75 2 32.895810 family 1, PF01407: Geminivirus AL3 protein Molecular characterization of the AL3 protein encoded by a family 2, PF08283: Geminivirus rep protein central domain The structure of a replication initiator unites diverse index pos1 pos2 score npdbs avgdist mindist nshort 0 145 82 14.470571 0 - - 0 1 145 83 18.425241 0 - - 0 #151 PF00380 PF00411 270 3 32.696789 family 1, PF00380: Ribosomal protein S9/S16 family 2, PF00411: Ribosomal protein S11 index pos1 pos2 score npdbs avgdist mindist nshort 0 372 38 10.453651 1 44.0786 44.0786 0 1 372 40 11.018420 1 41.3313 41.3313 0 2 372 99 11.224721 1 49.4949 49.4949 0 152 PF00177 PF04565 303 4 32.585006 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF04565: RNA polymerase Rpb2, domain 3 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 300 9 9.933894 0 - - 0 1 300 49 11.220085 0 - - 0 2 304 9 13.660150 0 - - 0 3 304 49 12.822129 0 - - 0 #153 PF02446 PF02684 63 3 32.491633 family 1, PF02446: 4-alpha-glucanotransferase Disproportionating enzyme (4-alpha-glucanotransferase; EC family 2, PF02684: Lipid-A-disaccharide synthetase Cloning and expression of genes encoding lipid A index pos1 pos2 score npdbs avgdist mindist nshort 0 529 134 13.366379 0 - - 0 1 529 165 9.465100 0 - - 0 2 667 134 9.660156 0 - - 0 154 PF00490 PF07475 50 4 32.231954 family 1, PF00490: Delta-aminolevulinic acid dehydratase family 2, PF07475: HPr Serine kinase C-terminus A novel protein kinase that controls carbon catabolite index pos1 pos2 score npdbs avgdist mindist nshort 0 143 33 11.180257 0 - - 0 1 143 171 9.871442 0 - - 0 2 151 33 11.180257 0 - - 0 3 151 171 9.871442 0 - - 0 155 PF02503 PF04355 52 3 32.010980 family 1, PF02503: Polyphosphate kinase Transcription of ppk from Acinetobacter sp. strain ADP1, family 2, PF04355: SmpA / OmlA family Pseudomonas aeruginosa fur overlaps with a gene encoding a index pos1 pos2 score npdbs avgdist mindist nshort 0 110 79 13.214407 0 - - 0 1 373 79 9.174032 0 - - 0 2 764 79 9.622544 0 - - 0 156 PF01264 PF01316 80 3 31.658617 family 1, PF01264: Chorismate synthase family 2, PF01316: Arginine repressor, DNA binding domain Solution structure of the DNA-binding domain and model for index pos1 pos2 score npdbs avgdist mindist nshort 0 108 46 9.586710 0 - - 0 1 207 46 10.070374 0 - - 0 2 217 46 12.001537 0 - - 0 #157 PF04561 PF04567 171 3 31.529872 family 1, PF04561: RNA polymerase Rpb2, domain 2 Structural basis of transcription: RNA polymerase II at 2.8 family 2, PF04567: RNA polymerase Rpb2, domain 5 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 65 103 10.327020 1 46.0006 46.0006 0 1 226 103 11.582333 1 41.0173 41.0173 0 2 332 0 9.620521 1 30.3416 30.3416 0 #158 PF00312 PF00347 251 4 31.267216 family 1, PF00312: Ribosomal protein S15 Conformational variability of the N-terminal helix in the family 2, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene index pos1 pos2 score npdbs avgdist mindist nshort 0 24 172 10.998729 0 - - 0 1 24 174 12.042668 0 - - 0 2 33 172 12.670260 0 - - 0 3 33 174 11.672305 0 - - 0 159 PF00490 PF01784 131 3 31.001325 family 1, PF00490: Delta-aminolevulinic acid dehydratase family 2, PF01784: NIF3 (NGG1p interacting factor 3) Transcriptional activation by yeast PDR1p is inhibited by index pos1 pos2 score npdbs avgdist mindist nshort 0 151 54 11.318261 0 - - 0 1 151 97 9.561684 0 - - 0 2 151 151 10.121383 0 - - 0 #160 PF00189 PF00411 309 3 30.856614 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF00411: Ribosomal protein S11 index pos1 pos2 score npdbs avgdist mindist nshort 0 10 40 10.572329 1 86.9175 86.9175 0 1 10 145 9.577580 1 86.1567 86.1567 0 2 91 38 10.706709 1 77.0641 77.0641 0 *161 PF00626 PF04815 48 3 29.858752 family 1, PF00626: Gelsolin repeat The crystal structure of plasma gelsolin: implications for family 2, PF04815: Sec23/Sec24 helical domain Structure of the Sec23p/24p and Sec13p/31p complexes of index pos1 pos2 score npdbs avgdist mindist nshort 0 8 7 10.319129 1 20.8165 20.8165 0 1 135 122 9.106389 1 31.7818 31.7818 0 2 211 7 10.433238 1 30.5090 30.5090 0 162 PF01964 PF06798 46 4 29.770541 family 1, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes family 2, PF06798: PrkA serine protein kinase C-terminal domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 306 353 9.969052 0 - - 0 1 306 356 10.624171 0 - - 0 2 323 353 9.177320 0 - - 0 3 323 356 9.094778 0 - - 0 163 PF00953 PF04293 51 3 29.665511 family 1, PF00953: Glycosyl transferase family 4 A family of UDP-GlcNAc/MurNAc: polyisoprenol-P family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 69 19 9.161137 0 - - 0 1 69 155 10.407796 0 - - 0 2 69 465 10.096582 0 - - 0 164 PF01977 PF02620 62 3 29.643866 family 1, PF01977: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Membrane-associated reactions in ubiquinone biosynthesis in family 2, PF02620: Uncharacterized ACR, COG1399 index pos1 pos2 score npdbs avgdist mindist nshort 0 294 292 9.181427 0 - - 0 1 324 292 10.181770 0 - - 0 2 632 292 10.280672 0 - - 0 165 PF00410 PF01509 227 3 29.567516 family 1, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein family 2, PF01509: TruB family pseudouridylate synthase (N terminal domain) Purification, cloning, and properties of the tRNA psi 55 index pos1 pos2 score npdbs avgdist mindist nshort 0 214 179 9.740686 0 - - 0 1 214 354 9.899330 0 - - 0 2 262 179 9.927502 0 - - 0 #166 PF00366 PF03947 261 3 29.182711 family 1, PF00366: Ribosomal protein S17 family 2, PF03947: Ribosomal Proteins L2, C-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 28 207 17.973591 0 - - 0 1 80 19 11.646874 0 - - 0 2 80 204 14.498387 0 - - 0 167 PF00587 PF08298 51 3 29.126213 family 1, PF00587: tRNA synthetase class II core domain (G, H, P, S and T) Eleven down and nine to go. family 2, PF08298: PrkA AAA domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 95 406 9.210875 0 - - 0 1 754 355 9.296628 0 - - 0 2 855 264 10.618710 0 - - 0 168 PF02390 PF03618 91 3 29.090336 family 1, PF02390: Putative methyltransferase family 2, PF03618: Domain of unknown function (DUF299) index pos1 pos2 score npdbs avgdist mindist nshort 0 441 285 10.691539 0 - - 0 1 581 285 9.220383 0 - - 0 2 598 285 9.178416 0 - - 0 *169 PF00680 PF00863 59 3 29.058488 family 1, PF00680: RNA dependent RNA polymerase family 2, PF00863: Peptidase family C4 index pos1 pos2 score npdbs avgdist mindist nshort 0 562 200 10.202577 0 - - 0 1 562 267 9.416679 0 - - 0 2 562 281 9.439236 0 - - 0 170 PF00623 PF00687 240 3 28.890033 family 1, PF00623: RNA polymerase Rpb1, domain 2 Structural modules of the large subunits of RNA polymerase. family 2, PF00687: Ribosomal protein L1p/L10e family index pos1 pos2 score npdbs avgdist mindist nshort 0 130 547 13.961638 0 - - 0 1 395 303 11.190054 0 - - 0 2 395 382 11.343344 0 - - 0 171 PF00365 PF03070 66 3 28.294269 family 1, PF00365: Phosphofructokinase family 2, PF03070: TENA/THI-4/PQQC family Cloning and characterization of a pair of novel genes that index pos1 pos2 score npdbs avgdist mindist nshort 0 15 44 9.841090 0 - - 0 1 15 267 9.068294 0 - - 0 2 54 44 9.384888 0 - - 0 172 PF00410 PF04998 289 2 28.240402 family 1, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein family 2, PF04998: RNA polymerase Rpb1, domain 5 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 214 37 14.694727 0 - - 0 1 214 56 13.545677 0 - - 0 *173 PF00182 PF00187 68 2 27.154936 family 1, PF00182: Chitinase class I family 2, PF00187: Chitin recognition protein index pos1 pos2 score npdbs avgdist mindist nshort 0 237 94 12.982262 0 - - 0 1 237 95 14.172677 0 - - 0 174 PF00793 PF03618 89 3 26.242809 family 1, PF00793: DAHP synthetase I family Crystal structure of phenylalanine-regulated family 2, PF03618: Domain of unknown function (DUF299) index pos1 pos2 score npdbs avgdist mindist nshort 0 176 268 10.030405 0 - - 0 1 187 285 9.872137 0 - - 0 2 283 285 9.181974 0 - - 0 #175 PF00177 PF00410 304 3 26.231426 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein index pos1 pos2 score npdbs avgdist mindist nshort 0 97 262 10.862506 0 - - 0 1 300 260 10.211155 0 - - 0 2 304 260 10.254353 0 - - 0 176 PF01632 PF03588 81 2 25.363453 family 1, PF01632: Ribosomal protein L35 family 2, PF03588: Leucyl/phenylalanyl-tRNA protein transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 30 16 13.569986 0 - - 0 1 32 16 11.793470 0 - - 0 *177 PF00174 PF03404 93 2 25.006852 family 1, PF00174: Oxidoreductase molybdopterin binding domain Molecular basis of sulfite oxidase deficiency from the family 2, PF03404: Mo-co oxidoreductase dimerisation domain Molecular basis of sulfite oxidase deficiency from the index pos1 pos2 score npdbs avgdist mindist nshort 0 140 65 13.624095 2 23.2464 21.9217 0 1 342 65 11.382759 2 13.2239 13.1837 0 178 PF00343 PF01209 106 2 24.745617 family 1, PF00343: Carbohydrate phosphorylase Control of phosphorylase b conformation by a modified family 2, PF01209: ubiE/COQ5 methyltransferase family index pos1 pos2 score npdbs avgdist mindist nshort 0 39 40 14.134196 0 - - 0 1 1647 40 10.611421 0 - - 0 179 PF00091 PF06418 224 2 24.596694 family 1, PF00091: Tubulin/FtsZ family, GTPase domain Structure of the alphabeta tubulin dimer by electron family 2, PF06418: CTP synthase N-terminus Thr-431 and Arg-433 are part of a conserved sequence motif index pos1 pos2 score npdbs avgdist mindist nshort 0 158 395 12.957714 0 - - 0 1 205 395 11.638982 0 - - 0 180 PF00270 PF04379 74 2 24.208208 family 1, PF00270: DEAD/DEAH box helicase Unwinding RNA in Saccharomyces cerevisiae: DEAD-box family 2, PF04379: Protein of unknown function (DUF525) A family of mammalian F-box proteins. index pos1 pos2 score npdbs avgdist mindist nshort 0 6 97 10.631547 0 - - 0 1 96 97 13.576661 0 - - 0 #181 PF00410 PF00411 309 2 23.753475 family 1, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein family 2, PF00411: Ribosomal protein S11 index pos1 pos2 score npdbs avgdist mindist nshort 0 214 48 12.446348 0 - - 0 1 262 152 11.307130 0 - - 0 *182 PF00270 PF00271 412 1 23.714894 family 1, PF00270: DEAD/DEAH box helicase Unwinding RNA in Saccharomyces cerevisiae: DEAD-box family 2, PF00271: Helicase conserved C-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 1067 340 23.714895 3 23.6950 21.9081 0 183 PF04997 PF06421 212 2 23.637029 family 1, PF04997: RNA polymerase Rpb1, domain 1 Structural modules of the large subunits of RNA polymerase. family 2, PF06421: GTP-binding protein LepA C-terminus Evolution of a molecular switch: universal bacterial index pos1 pos2 score npdbs avgdist mindist nshort 0 24 72 11.942279 0 - - 0 1 1545 72 11.694751 0 - - 0 #184 PF00164 PF00203 328 2 23.092780 family 1, PF00164: Ribosomal protein S12 family 2, PF00203: Ribosomal protein S19 index pos1 pos2 score npdbs avgdist mindist nshort 0 109 129 13.646113 1 75.1613 75.1613 0 1 183 129 9.446670 1 81.7627 81.7627 0 185 PF01175 PF06071 74 2 23.023508 family 1, PF01175: Urocanase family 2, PF06071: Protein of unknown function (DUF933) index pos1 pos2 score npdbs avgdist mindist nshort 0 820 75 12.350922 0 - - 0 1 820 111 10.672587 0 - - 0 *186 PF01565 PF02873 170 2 23.021027 family 1, PF01565: FAD binding domain Crystal structures and inhibitor binding in the octameric family 2, PF02873: UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain The structure of the substrate-free form of MurB, an index pos1 pos2 score npdbs avgdist mindist nshort 0 335 179 13.596686 1 12.5224 12.5224 0 1 337 179 9.424342 1 12.8088 12.8088 0 187 PF02446 PF02873 86 2 22.962762 family 1, PF02446: 4-alpha-glucanotransferase Disproportionating enzyme (4-alpha-glucanotransferase; EC family 2, PF02873: UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain The structure of the substrate-free form of MurB, an index pos1 pos2 score npdbs avgdist mindist nshort 0 529 43 12.354782 0 - - 0 1 529 203 10.607980 0 - - 0 188 PF01717 PF03814 57 2 22.760431 family 1, PF01717: Cobalamin-independent synthase, Catalytic domain The specific features of methionine biosynthesis and family 2, PF03814: Potassium-transporting ATPase A subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 447 141 11.346929 0 - - 0 1 447 163 11.413505 0 - - 0 189 PF02742 PF06723 47 2 22.716418 family 1, PF02742: Iron dependent repressor, metal binding and dimerisation domain Structures of the apo- and the metal ion-activated forms of family 2, PF06723: MreB/Mbl protein Cytoskeletons in prokaryotes. index pos1 pos2 score npdbs avgdist mindist nshort 0 38 162 9.810278 0 - - 0 1 38 305 12.906143 0 - - 0 190 PF00347 PF04998 258 2 22.671406 family 1, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene family 2, PF04998: RNA polymerase Rpb1, domain 5 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 179 37 12.076532 0 - - 0 1 179 56 10.594876 0 - - 0 191 PF00281 PF04565 266 2 22.494382 family 1, PF00281: Ribosomal protein L5 family 2, PF04565: RNA polymerase Rpb2, domain 3 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 7 9 12.283290 0 - - 0 1 7 49 10.211093 0 - - 0 *192 PF07662 PF07670 80 2 22.431001 family 1, PF07662: Na+ dependent nucleoside transporter C-terminus Primary structure and functional expression of a cDNA family 2, PF07670: Nucleoside recognition Identification of amino acid residues responsible for the index pos1 pos2 score npdbs avgdist mindist nshort 0 92 399 11.937716 0 - - 0 1 207 498 10.493287 0 - - 0 193 PF00793 PF04401 46 3 22.357777 family 1, PF00793: DAHP synthetase I family Crystal structure of phenylalanine-regulated family 2, PF04401: Protein of unknown function (DUF540) index pos1 pos2 score npdbs avgdist mindist nshort 0 238 163 9.401945 0 - - 0 1 472 95 9.791444 0 - - 0 2 472 163 11.571108 0 - - 0 #194 PF00163 PF00410 270 2 22.109281 family 1, PF00163: Ribosomal protein S4/S9 N-terminal domain The crystal structure of ribosomal protein S4 reveals a family 2, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein index pos1 pos2 score npdbs avgdist mindist nshort 0 102 214 9.401711 0 - - 0 1 132 214 12.707570 0 - - 0 195 PF02572 PF02777 83 2 22.071976 family 1, PF02572: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP Cobalamin (vitamin B12) biosynthesis: identification and family 2, PF02777: Iron/manganese superoxide dismutases, C-terminal domain Refined crystal structure of a superoxide dismutase from index pos1 pos2 score npdbs avgdist mindist nshort 0 158 61 10.339809 0 - - 0 1 159 61 11.732169 0 - - 0 196 PF00764 PF03746 76 2 22.031783 family 1, PF00764: Arginosuccinate synthase A P-loop-like motif in a widespread ATP pyrophosphatase family 2, PF03746: LamB/YcsF family Molecular characterization of the lam locus and sequences index pos1 pos2 score npdbs avgdist mindist nshort 0 134 78 9.660922 0 - - 0 1 484 78 12.370864 0 - - 0 197 PF01175 PF02223 74 2 22.019360 family 1, PF01175: Urocanase family 2, PF02223: Thymidylate kinase index pos1 pos2 score npdbs avgdist mindist nshort 0 751 89 9.096156 0 - - 0 1 820 89 12.923206 0 - - 0 198 PF00344 PF00347 255 2 21.978822 family 1, PF00344: eubacterial secY protein family 2, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene index pos1 pos2 score npdbs avgdist mindist nshort 0 11 179 11.976220 0 - - 0 1 38 179 10.002603 0 - - 0 199 PF00342 PF04293 52 2 21.874906 family 1, PF00342: Phosphoglucose isomerase Crystallographic structure analysis of glucose 6-phosphate family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 400 465 11.166336 0 - - 0 1 403 465 10.708571 0 - - 0 200 PF00490 PF03350 53 2 21.863952 family 1, PF00490: Delta-aminolevulinic acid dehydratase family 2, PF03350: Uncharacterized protein family, UPF0114 index pos1 pos2 score npdbs avgdist mindist nshort 0 143 90 10.931977 0 - - 0 1 151 90 10.931977 0 - - 0 #201 PF00164 PF00189 317 2 21.851315 family 1, PF00164: Ribosomal protein S12 family 2, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of index pos1 pos2 score npdbs avgdist mindist nshort 0 121 10 9.521077 1 38.3518 38.3518 0 1 140 102 12.330240 1 71.0129 71.0129 0 #202 PF00298 PF00411 264 2 21.835162 family 1, PF00298: Ribosomal protein L11, RNA binding domain High resolution solution structure of ribosomal protein family 2, PF00411: Ribosomal protein S11 index pos1 pos2 score npdbs avgdist mindist nshort 0 0 38 9.147173 0 - - 0 1 92 38 12.687990 0 - - 0 #203 PF00203 PF00411 318 2 21.790348 family 1, PF00203: Ribosomal protein S19 family 2, PF00411: Ribosomal protein S11 index pos1 pos2 score npdbs avgdist mindist nshort 0 77 40 10.217277 1 86.4084 86.4084 0 1 77 99 11.573072 1 96.2062 96.2062 0 204 PF01450 PF06434 60 2 21.695099 family 1, PF01450: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid family 2, PF06434: Aconitate hydratase 2 N-terminus Biochemical and spectroscopic characterization of index pos1 pos2 score npdbs avgdist mindist nshort 0 206 445 9.692881 0 - - 0 1 314 445 12.002220 0 - - 0 *205 PF01074 PF07748 55 2 21.615078 family 1, PF01074: Glycosyl hydrolases family 38 N-terminal domain Glycosidase families family 2, PF07748: Glycosyl hydrolases family 38 C-terminal domain Glycosidase families index pos1 pos2 score npdbs avgdist mindist nshort 0 274 811 10.716400 1 23.9211 23.9211 0 1 501 811 10.898679 1 43.7207 43.7207 0 206 PF01964 PF01975 97 2 21.580565 family 1, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes family 2, PF01975: Survival protein SurE A new gene involved in stationary-phase survival located at index pos1 pos2 score npdbs avgdist mindist nshort 0 306 73 10.801248 0 - - 0 1 306 78 10.779319 0 - - 0 207 PF00344 PF04565 260 2 21.445942 family 1, PF00344: eubacterial secY protein family 2, PF04565: RNA polymerase Rpb2, domain 3 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 852 9 9.950706 0 - - 0 1 852 49 11.495237 0 - - 0 #208 PF01293 PF03668 49 2 21.415677 family 1, PF01293: Phosphoenolpyruvate carboxykinase Snapshot of an enzyme reaction intermediate in the family 2, PF03668: P-loop ATPase protein family index pos1 pos2 score npdbs avgdist mindist nshort 0 100 269 9.758475 0 - - 0 1 179 269 11.657204 0 - - 0 #209 PF00203 PF00281 284 2 21.284240 family 1, PF00203: Ribosomal protein S19 family 2, PF00281: Ribosomal protein L5 index pos1 pos2 score npdbs avgdist mindist nshort 0 137 7 10.020070 0 - - 0 1 137 19 11.264172 0 - - 0 210 PF02401 PF02572 79 2 21.133236 family 1, PF02401: LytB protein Identification of the Escherichia coli lytB gene, which is family 2, PF02572: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP Cobalamin (vitamin B12) biosynthesis: identification and index pos1 pos2 score npdbs avgdist mindist nshort 0 5 162 9.696281 0 - - 0 1 10 162 11.436958 0 - - 0 #211 PF01654 PF02322 123 2 21.122344 family 1, PF01654: Bacterial Cytochrome Ubiquinol Oxidase The Klebsiella pneumoniae cytochrome bd' terminal oxidase family 2, PF02322: Cytochrome oxidase subunit II The Klebsiella pneumoniae cytochrome bd' terminal oxidase index pos1 pos2 score npdbs avgdist mindist nshort 0 213 81 10.986255 0 - - 0 1 213 95 10.136091 0 - - 0 212 PF00271 PF00680 51 2 21.084839 family 1, PF00271: Helicase conserved C-terminal domain family 2, PF00680: RNA dependent RNA polymerase index pos1 pos2 score npdbs avgdist mindist nshort 0 128 204 10.307351 0 - - 0 1 128 835 10.777489 0 - - 0 213 PF01612 PF04608 70 2 21.053881 family 1, PF01612: 3'-5' exonuclease Structure of large fragment of Escherichia coli DNA family 2, PF04608: Phosphatidylglycerophosphatase A The pgpA and pgpB genes of Escherichia coli are not index pos1 pos2 score npdbs avgdist mindist nshort 0 566 12 9.269978 0 - - 0 1 615 12 11.783905 0 - - 0 #214 PF00181 PF00410 311 2 20.952185 family 1, PF00181: Ribosomal Proteins L2, RNA binding domain family 2, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein index pos1 pos2 score npdbs avgdist mindist nshort 0 6 262 10.939440 0 - - 0 1 15 262 10.012747 0 - - 0 #215 PF00380 PF00679 250 2 20.901113 family 1, PF00380: Ribosomal protein S9/S16 family 2, PF00679: Elongation factor G C-terminus index pos1 pos2 score npdbs avgdist mindist nshort 0 344 423 10.021093 0 - - 0 1 345 423 10.880021 0 - - 0 #216 PF00347 PF00380 257 2 20.874113 family 1, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene family 2, PF00380: Ribosomal protein S9/S16 index pos1 pos2 score npdbs avgdist mindist nshort 0 165 372 11.034208 0 - - 0 1 179 372 9.839906 0 - - 0 217 PF00177 PF00623 241 2 20.762232 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF00623: RNA polymerase Rpb1, domain 2 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 25 52 9.474865 0 - - 0 1 281 395 11.287367 0 - - 0 #218 PF00189 PF01020 64 2 20.759027 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF01020: Ribosomal L40e family RNA binding proteins of the large subunit of bovine index pos1 pos2 score npdbs avgdist mindist nshort 0 20 14 10.039379 0 - - 0 1 123 14 10.719651 0 - - 0 219 PF03313 PF03550 46 2 20.705520 family 1, PF03313: Serine dehydratase alpha chain family 2, PF03550: Outer membrane lipoprotein LolB index pos1 pos2 score npdbs avgdist mindist nshort 0 434 156 11.269734 0 - - 0 1 505 156 9.435786 0 - - 0 220 PF01175 PF01411 73 2 20.696120 family 1, PF01175: Urocanase family 2, PF01411: tRNA synthetases class II (A) index pos1 pos2 score npdbs avgdist mindist nshort 0 820 124 10.009948 0 - - 0 1 820 127 10.686174 0 - - 0 *221 PF00984 PF03720 192 1 20.688377 family 1, PF00984: UDP-glucose/GDP-mannose dehydrogenase family, central domain Purification and characterization of guanosine family 2, PF03720: UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain Purification and characterization of guanosine index pos1 pos2 score npdbs avgdist mindist nshort 0 14 194 20.688379 1 30.7651 30.7651 0 222 PF01510 PF04898 87 2 20.671841 family 1, PF01510: N-acetylmuramoyl-L-alanine amidase Cloning, sequencing and expression of a Bacillus family 2, PF04898: Glutamate synthase central domain Structural studies on the synchronization of catalytic index pos1 pos2 score npdbs avgdist mindist nshort 0 462 87 9.557021 0 - - 0 1 462 360 11.114823 0 - - 0 223 PF00091 PF01175 78 2 20.620690 family 1, PF00091: Tubulin/FtsZ family, GTPase domain Structure of the alphabeta tubulin dimer by electron family 2, PF01175: Urocanase index pos1 pos2 score npdbs avgdist mindist nshort 0 354 820 10.012576 0 - - 0 1 444 820 10.608114 0 - - 0 224 PF00238 PF04565 290 2 20.606915 family 1, PF00238: Ribosomal protein L14p/L23e family 2, PF04565: RNA polymerase Rpb2, domain 3 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 259 9 11.145607 0 - - 0 1 318 9 9.461311 0 - - 0 #225 PF01432 PF01894 72 2 20.535530 family 1, PF01432: Peptidase family M3 Evolutionary families of metallopeptidases. family 2, PF01894: Uncharacterised protein family UPF0047 index pos1 pos2 score npdbs avgdist mindist nshort 0 719 173 11.193795 0 - - 0 1 739 173 9.341738 0 - - 0 226 PF01432 PF01964 103 2 20.501468 family 1, PF01432: Peptidase family M3 Evolutionary families of metallopeptidases. family 2, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes index pos1 pos2 score npdbs avgdist mindist nshort 0 739 157 9.181490 0 - - 0 1 1030 306 11.319980 0 - - 0 227 PF01523 PF02401 97 2 20.441912 family 1, PF01523: Putative modulator of DNA gyrase Evidence for involvement of Escherichia coli genes pmbA, family 2, PF02401: LytB protein Identification of the Escherichia coli lytB gene, which is index pos1 pos2 score npdbs avgdist mindist nshort 0 353 218 9.025303 0 - - 0 1 545 218 11.416612 0 - - 0 228 PF02867 PF04362 46 2 20.410941 family 1, PF02867: Ribonucleotide reductase, barrel domain Structure of ribonucleotide reductase protein R1. family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 338 20 9.741628 0 - - 0 1 361 20 10.669315 0 - - 0 229 PF01977 PF02401 86 2 20.342313 family 1, PF01977: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Membrane-associated reactions in ubiquinone biosynthesis in family 2, PF02401: LytB protein Identification of the Escherichia coli lytB gene, which is index pos1 pos2 score npdbs avgdist mindist nshort 0 511 518 9.603234 0 - - 0 1 625 518 10.739081 0 - - 0 230 PF01980 PF02091 46 2 20.269707 family 1, PF01980: Uncharacterised protein family UPF0066 family 2, PF02091: Glycyl-tRNA synthetase alpha subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 2 213 10.564816 0 - - 0 1 262 213 9.704894 0 - - 0 231 PF00120 PF01175 78 2 20.159251 family 1, PF00120: Glutamine synthetase, catalytic domain family 2, PF01175: Urocanase index pos1 pos2 score npdbs avgdist mindist nshort 0 278 820 10.518682 0 - - 0 1 296 820 9.640571 0 - - 0 232 PF01208 PF01985 76 2 20.111832 family 1, PF01208: Uroporphyrinogen decarboxylase (URO-D) family 2, PF01985: CRS1 / YhbY domain Crystal structure of E. coli YhbY: a representative of a index pos1 pos2 score npdbs avgdist mindist nshort 0 158 61 10.841904 0 - - 0 1 164 61 9.269929 0 - - 0 *233 PF01154 PF08540 79 2 20.111329 family 1, PF01154: Hydroxymethylglutaryl-coenzyme A synthase N terminal Amino acid sequence of an active site peptide of avian family 2, PF08540: Hydroxymethylglutaryl-coenzyme A synthase C terminal Amino acid sequence of an active site peptide of avian index pos1 pos2 score npdbs avgdist mindist nshort 0 49 260 10.590855 1 14.2804 14.2804 0 1 261 18 9.520477 1 12.9784 12.9784 0 234 PF02153 PF04362 46 2 20.084356 family 1, PF02153: Prephenate dehydrogenase family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 591 19 9.338776 0 - - 0 1 591 83 10.745581 0 - - 0 235 PF01264 PF04293 50 2 19.951836 family 1, PF01264: Chorismate synthase family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 230 539 9.549040 0 - - 0 1 364 508 10.402798 0 - - 0 236 PF00203 PF00344 257 2 19.897235 family 1, PF00203: Ribosomal protein S19 family 2, PF00344: eubacterial secY protein index pos1 pos2 score npdbs avgdist mindist nshort 0 77 38 10.501757 0 - - 0 1 129 856 9.395481 0 - - 0 *237 PF00081 PF02777 520 1 19.782422 family 1, PF00081: Iron/manganese superoxide dismutases, alpha-hairpin domain Refined crystal structure of a superoxide dismutase from family 2, PF02777: Iron/manganese superoxide dismutases, C-terminal domain Refined crystal structure of a superoxide dismutase from index pos1 pos2 score npdbs avgdist mindist nshort 0 157 61 19.782422 14 3.6816 0.1294 14 238 PF01458 PF01964 87 2 19.725079 family 1, PF01458: Uncharacterized protein family (UPF0051) family 2, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes index pos1 pos2 score npdbs avgdist mindist nshort 0 141 541 9.180218 0 - - 0 1 306 20 10.544862 0 - - 0 239 PF03548 PF03737 52 2 19.690852 family 1, PF03548: Outer membrane lipoprotein carrier protein LolA family 2, PF03737: Demethylmenaquinone methyltransferase Identification of a novel gene cluster participating in index pos1 pos2 score npdbs avgdist mindist nshort 0 153 208 10.075453 0 - - 0 1 153 355 9.615399 0 - - 0 #240 PF00164 PF00410 307 2 19.633426 family 1, PF00164: Ribosomal protein S12 family 2, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein index pos1 pos2 score npdbs avgdist mindist nshort 0 106 214 9.637644 0 - - 0 1 206 262 9.995784 0 - - 0 *241 PF00587 PF03129 268 2 19.600075 family 1, PF00587: tRNA synthetase class II core domain (G, H, P, S and T) Eleven down and nine to go. family 2, PF03129: Anticodon binding domain Evolution of aminoacyl-tRNA synthetases--analysis of unique index pos1 pos2 score npdbs avgdist mindist nshort 0 652 115 9.302201 7 31.0687 27.1344 0 1 758 115 10.297876 7 29.3610 22.2661 0 242 PF01450 PF04362 46 2 19.552032 family 1, PF01450: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 311 20 10.022004 0 - - 0 1 314 20 9.530031 0 - - 0 243 PF01450 PF02091 97 2 19.523871 family 1, PF01450: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid family 2, PF02091: Glycyl-tRNA synthetase alpha subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 18 45 9.989260 0 - - 0 1 180 45 9.534613 0 - - 0 244 PF00762 PF01175 66 2 19.479938 family 1, PF00762: Ferrochelatase family 2, PF01175: Urocanase index pos1 pos2 score npdbs avgdist mindist nshort 0 205 781 9.067327 0 - - 0 1 205 812 10.412612 0 - - 0 *245 PF00454 PF00613 48 2 19.416716 family 1, PF00454: Phosphatidylinositol 3- and 4-kinase Elucidating TOR signaling and rapamycin action: lessons family 2, PF00613: Phosphoinositide 3-kinase family, accessory domain (PIK domain) Using structure to define the function of phosphoinositide index pos1 pos2 score npdbs avgdist mindist nshort 0 48 4 10.248035 2 44.9211 43.5122 0 1 715 4 9.168681 2 57.6047 56.1198 0 #246 PF02965 PF05191 67 2 19.163275 family 1, PF02965: Vitamin B12 dependent methionine synthase, activation domain The structure of the C-terminal domain of methionine family 2, PF05191: Adenylate kinase, active site lid Crystal structures of Bacillus stearothermophilus adenylate index pos1 pos2 score npdbs avgdist mindist nshort 0 103 44 9.108494 0 - - 0 1 103 47 10.054783 0 - - 0 247 PF01977 PF02781 69 2 19.059334 family 1, PF01977: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Membrane-associated reactions in ubiquinone biosynthesis in family 2, PF02781: Glucose-6-phosphate dehydrogenase, C-terminal domain On the mechanism of the reaction catalyzed by glucose index pos1 pos2 score npdbs avgdist mindist nshort 0 327 237 9.591599 0 - - 0 1 568 237 9.467737 0 - - 0 248 PF00573 PF04293 52 2 19.019873 family 1, PF00573: Ribosomal protein L4/L1 family Yeast ribosomal proteins L4, L17, L20, and L25 exhibit family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 52 133 9.264932 0 - - 0 1 52 353 9.754943 0 - - 0 249 PF01450 PF04279 55 2 18.902826 family 1, PF01450: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid family 2, PF04279: Intracellular septation protein A Identification and characterization of ispA, a Shigella index pos1 pos2 score npdbs avgdist mindist nshort 0 311 211 9.311138 0 - - 0 1 314 211 9.591691 0 - - 0 250 PF01619 PF01977 74 2 18.857273 family 1, PF01619: Proline dehydrogenase Sequence analysis identifies the proline dehydrogenase and family 2, PF01977: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Membrane-associated reactions in ubiquinone biosynthesis in index pos1 pos2 score npdbs avgdist mindist nshort 0 477 627 9.673327 0 - - 0 1 927 643 9.183949 0 - - 0 251 PF00816 PF00977 46 2 18.800678 family 1, PF00816: H-NS histone family Solution structure of the DNA binding domain of a family 2, PF00977: Histidine biosynthesis protein Paralogous histidine biosynthetic genes: evolutionary index pos1 pos2 score npdbs avgdist mindist nshort 0 157 69 9.130121 0 - - 0 1 157 261 9.670558 0 - - 0 252 PF00762 PF01784 124 2 18.797636 family 1, PF00762: Ferrochelatase family 2, PF01784: NIF3 (NGG1p interacting factor 3) Transcriptional activation by yeast PDR1p is inhibited by index pos1 pos2 score npdbs avgdist mindist nshort 0 96 97 9.024844 0 - - 0 1 96 151 9.772794 0 - - 0 253 PF01832 PF01964 60 2 18.783578 family 1, PF01832: Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase Peptidoglycan-hydrolyzing activity of the FlgJ protein, family 2, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes index pos1 pos2 score npdbs avgdist mindist nshort 0 111 307 9.299258 0 - - 0 1 174 306 9.484323 0 - - 0 254 PF00953 PF04285 49 2 18.667435 family 1, PF00953: Glycosyl transferase family 4 A family of UDP-GlcNAc/MurNAc: polyisoprenol-P family 2, PF04285: Protein of unknown function (DUF444) index pos1 pos2 score npdbs avgdist mindist nshort 0 69 183 9.181525 0 - - 0 1 69 446 9.485911 0 - - 0 255 PF01411 PF01790 183 2 18.665288 family 1, PF01411: tRNA synthetases class II (A) family 2, PF01790: Prolipoprotein diacylglyceryl transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 94 565 9.640479 0 - - 0 1 1449 565 9.024810 0 - - 0 $256 PF04941 PF05094 80 2 18.642672 family 1, PF04941: Late expression factor 8 (LEF-8) Characterization of late gene expression factors lef-9 and family 2, PF05094: Late expression factor 9 (LEF-9) Characterization of late gene expression factors lef-9 and index pos1 pos2 score npdbs avgdist mindist nshort 0 626 238 9.049536 0 - - 0 1 626 284 9.593138 0 - - 0 257 PF01977 PF02091 85 2 18.639274 family 1, PF01977: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Membrane-associated reactions in ubiquinone biosynthesis in family 2, PF02091: Glycyl-tRNA synthetase alpha subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 713 150 9.290765 0 - - 0 1 753 150 9.348510 0 - - 0 258 PF00317 PF03313 108 2 18.564251 family 1, PF00317: Ribonucleotide reductase, all-alpha domain Structure of ribonucleotide reductase protein R1. family 2, PF03313: Serine dehydratase alpha chain index pos1 pos2 score npdbs avgdist mindist nshort 0 177 307 9.410741 0 - - 0 1 177 483 9.153510 0 - - 0 259 PF01980 PF02873 52 2 18.527220 family 1, PF01980: Uncharacterised protein family UPF0066 family 2, PF02873: UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain The structure of the substrate-free form of MurB, an index pos1 pos2 score npdbs avgdist mindist nshort 0 95 11 9.307035 0 - - 0 1 95 125 9.220186 0 - - 0 *260 PF00562 PF04560 437 2 18.496506 family 1, PF00562: RNA polymerase Rpb2, domain 6 Structural basis of transcription: RNA polymerase II at 2.8 family 2, PF04560: RNA polymerase Rpb2, domain 7 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 872 3 9.383028 2 30.9526 30.0789 0 1 1230 25 9.113479 2 8.0495 3.3636 1 261 PF00573 PF01316 82 2 18.429768 family 1, PF00573: Ribosomal protein L4/L1 family Yeast ribosomal proteins L4, L17, L20, and L25 exhibit family 2, PF01316: Arginine repressor, DNA binding domain Solution structure of the DNA-binding domain and model for index pos1 pos2 score npdbs avgdist mindist nshort 0 151 46 9.282793 0 - - 0 1 154 56 9.146977 0 - - 0 262 PF00303 PF02554 68 2 18.305525 family 1, PF00303: Thymidylate synthase family 2, PF02554: Carbon starvation protein CstA Molecular and functional characterization of a carbon index pos1 pos2 score npdbs avgdist mindist nshort 0 657 471 9.010037 0 - - 0 1 742 471 9.295490 0 - - 0 263 PF04293 PF06798 51 2 18.194004 family 1, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus family 2, PF06798: PrkA serine protein kinase C-terminal domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 19 26 9.115737 0 - - 0 1 148 26 9.078268 0 - - 0 264 PF00411 PF04565 294 1 18.182561 family 1, PF00411: Ribosomal protein S11 family 2, PF04565: RNA polymerase Rpb2, domain 3 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 29 29 18.182562 0 - - 0 265 PF01175 PF02401 61 2 18.120575 family 1, PF01175: Urocanase family 2, PF02401: LytB protein Identification of the Escherichia coli lytB gene, which is index pos1 pos2 score npdbs avgdist mindist nshort 0 805 165 9.038865 0 - - 0 1 805 346 9.081712 0 - - 0 *266 PF00753 PF07521 201 1 17.272898 family 1, PF00753: Metallo-beta-lactamase superfamily Extracting protein alignment models from the sequence family 2, PF07521: RNA-metabolising metallo-beta-lactamase Metallo-beta-lactamase fold within nucleic acids processing index pos1 pos2 score npdbs avgdist mindist nshort 0 417 41 17.272899 0 - - 0 #267 PF00119 PF00507 946 1 17.124269 family 1, PF00119: ATP synthase A chain family 2, PF00507: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 index pos1 pos2 score npdbs avgdist mindist nshort 0 315 119 17.124270 0 - - 0 268 PF00281 PF00707 194 1 16.395306 family 1, PF00281: Ribosomal protein L5 family 2, PF00707: Translation initiation factor IF-3, C-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 4 10 16.395307 0 - - 0 *269 PF02878 PF02879 281 1 15.382495 family 1, PF02878: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I The crystal structure of muscle phosphoglucomutase refined family 2, PF02879: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II The crystal structure of muscle phosphoglucomutase refined index pos1 pos2 score npdbs avgdist mindist nshort 0 243 175 15.382496 3 6.6856 5.9269 3 *270 PF03720 PF03721 192 1 14.968616 family 1, PF03720: UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain Purification and characterization of guanosine family 2, PF03721: UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain Purification and characterization of guanosine index pos1 pos2 score npdbs avgdist mindist nshort 0 194 547 14.968616 1 34.4421 34.4421 0 #271 PF00799 PF01492 64 1 14.899033 family 1, PF00799: Geminivirus Rep catalytic domain The structure of a replication initiator unites diverse family 2, PF01492: Geminivirus C4 protein Movement of tomato yellow leaf curl geminivirus (TYLCV): index pos1 pos2 score npdbs avgdist mindist nshort 0 154 61 14.899034 0 - - 0 272 PF00318 PF04355 70 1 14.767070 family 1, PF00318: Ribosomal protein S2 family 2, PF04355: SmpA / OmlA family Pseudomonas aeruginosa fur overlaps with a gene encoding a index pos1 pos2 score npdbs avgdist mindist nshort 0 169 79 14.767071 0 - - 0 273 PF01180 PF02624 52 1 14.614354 family 1, PF01180: Dihydroorotate dehydrogenase The crystal structure of Lactococcus lactis dihydroorotate family 2, PF02624: YcaO-like family index pos1 pos2 score npdbs avgdist mindist nshort 0 59 189 14.614354 0 - - 0 #274 PF00318 PF00679 254 1 14.506881 family 1, PF00318: Ribosomal protein S2 family 2, PF00679: Elongation factor G C-terminus index pos1 pos2 score npdbs avgdist mindist nshort 0 9 423 14.506882 0 - - 0 275 PF00204 PF00471 187 1 13.930852 family 1, PF00204: DNA gyrase B Crystal structure of an N-terminal fragment of the DNA family 2, PF00471: Ribosomal protein L33 index pos1 pos2 score npdbs avgdist mindist nshort 0 126 53 13.930852 0 - - 0 #276 PF00380 PF00410 266 1 13.847528 family 1, PF00380: Ribosomal protein S9/S16 family 2, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein index pos1 pos2 score npdbs avgdist mindist nshort 0 372 214 13.847528 0 - - 0 *277 PF01077 PF03460 270 1 13.770974 family 1, PF01077: Nitrite and sulphite reductase 4Fe-4S domain Sulfite reductase structure at 1.6 A: evolution and family 2, PF03460: Nitrite/Sulfite reductase ferredoxin-like half domain Sulfite reductase structure at 1.6 A: evolution and index pos1 pos2 score npdbs avgdist mindist nshort 0 161 37 13.770974 0 - - 0 *278 PF04983 PF04997 319 1 13.734997 family 1, PF04983: RNA polymerase Rpb1, domain 3 Structural modules of the large subunits of RNA polymerase. family 2, PF04997: RNA polymerase Rpb1, domain 1 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 22 1576 13.734999 2 82.8553 78.1898 0 279 PF00252 PF01964 116 1 13.676528 family 1, PF00252: Ribosomal protein L16 family 2, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes index pos1 pos2 score npdbs avgdist mindist nshort 0 150 306 13.676528 0 - - 0 280 PF00816 PF01553 46 1 13.584431 family 1, PF00816: H-NS histone family Solution structure of the DNA binding domain of a family 2, PF01553: Acyltransferase Barth syndrome may be due to an acyltransferase deficiency. index pos1 pos2 score npdbs avgdist mindist nshort 0 157 118 13.584432 0 - - 0 281 PF00889 PF08278 52 1 13.489897 family 1, PF00889: Elongation factor TS family 2, PF08278: DNA primase DnaG DnaB-binding Identification of a domain of Escherichia coli primase index pos1 pos2 score npdbs avgdist mindist nshort 0 558 91 13.489899 0 - - 0 282 PF02934 PF03618 77 1 13.463066 family 1, PF02934: PET112 family, N terminal region family 2, PF03618: Domain of unknown function (DUF299) index pos1 pos2 score npdbs avgdist mindist nshort 0 168 285 13.463067 0 - - 0 *283 PF00623 PF05000 388 1 13.373974 family 1, PF00623: RNA polymerase Rpb1, domain 2 Structural modules of the large subunits of RNA polymerase. family 2, PF05000: RNA polymerase Rpb1, domain 4 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 385 19 13.373975 2 45.8094 41.4117 0 284 PF02446 PF02542 81 1 13.342162 family 1, PF02446: 4-alpha-glucanotransferase Disproportionating enzyme (4-alpha-glucanotransferase; EC family 2, PF02542: YgbB family Biosynthesis of terpenoids: YgbB protein converts index pos1 pos2 score npdbs avgdist mindist nshort 0 386 132 13.342162 0 - - 0 285 PF01493 PF02572 80 1 13.334406 family 1, PF01493: GXGXG motif The formylmethanofuran dehydrogenase isoenzymes in family 2, PF02572: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP Cobalamin (vitamin B12) biosynthesis: identification and index pos1 pos2 score npdbs avgdist mindist nshort 0 279 162 13.334407 0 - - 0 286 PF01964 PF02934 103 1 13.280798 family 1, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes family 2, PF02934: PET112 family, N terminal region index pos1 pos2 score npdbs avgdist mindist nshort 0 306 23 13.280799 0 - - 0 *287 PF04329 PF04330 56 1 13.262847 family 1, PF04329: Family of unknown function (DUF470) Staphylococcus aureus resistance to human defensins and family 2, PF04330: Family of unknown function (DUF471) Staphylococcus aureus resistance to human defensins and index pos1 pos2 score npdbs avgdist mindist nshort 0 28 37 13.262848 0 - - 0 288 PF03548 PF04362 51 1 13.118915 family 1, PF03548: Outer membrane lipoprotein carrier protein LolA family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 153 20 13.118916 0 - - 0 289 PF01523 PF02965 69 1 13.079144 family 1, PF01523: Putative modulator of DNA gyrase Evidence for involvement of Escherichia coli genes pmbA, family 2, PF02965: Vitamin B12 dependent methionine synthase, activation domain The structure of the C-terminal domain of methionine index pos1 pos2 score npdbs avgdist mindist nshort 0 337 110 13.079144 0 - - 0 #290 PF00238 PF00318 296 1 12.961607 family 1, PF00238: Ribosomal protein L14p/L23e family 2, PF00318: Ribosomal protein S2 index pos1 pos2 score npdbs avgdist mindist nshort 0 259 20 12.961608 0 - - 0 291 PF02578 PF03588 77 1 12.896506 family 1, PF02578: Uncharacterised ACR, YfiH family COG1496 family 2, PF03588: Leucyl/phenylalanyl-tRNA protein transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 540 35 12.896506 0 - - 0 292 PF00411 PF04998 292 1 12.568496 family 1, PF00411: Ribosomal protein S11 family 2, PF04998: RNA polymerase Rpb1, domain 5 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 29 37 12.568498 0 - - 0 293 PF01175 PF01653 67 1 12.563070 family 1, PF01175: Urocanase family 2, PF01653: NAD-dependent DNA ligase adenylation domain Crystal structure of NAD(+)-dependent DNA ligase: modular index pos1 pos2 score npdbs avgdist mindist nshort 0 820 158 12.563071 0 - - 0 294 PF01384 PF03104 73 1 12.556601 family 1, PF01384: Phosphate transporter family Repressible cation-phosphate symporters in Neurospora family 2, PF03104: DNA polymerase family B, exonuclease domain Crystal structures of an NH2-terminal fragment of T4 DNA index pos1 pos2 score npdbs avgdist mindist nshort 0 2079 1723 12.556602 0 - - 0 295 PF00316 PF01964 65 1 12.541392 family 1, PF00316: Fructose-1-6-bisphosphatase Structure of rabbit liver fructose 1,6-bisphosphatase at family 2, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes index pos1 pos2 score npdbs avgdist mindist nshort 0 205 326 12.541393 0 - - 0 296 PF02636 PF03618 49 1 12.509233 family 1, PF02636: Uncharacterized ACR, COG1565 family 2, PF03618: Domain of unknown function (DUF299) index pos1 pos2 score npdbs avgdist mindist nshort 0 13 285 12.509234 0 - - 0 297 PF01175 PF01725 77 1 12.487750 family 1, PF01175: Urocanase family 2, PF01725: Ham1 family HAM1, the gene controlling 6-N-hydroxylaminopurine index pos1 pos2 score npdbs avgdist mindist nshort 0 571 8 12.487751 0 - - 0 298 PF00091 PF00177 246 1 12.450261 family 1, PF00091: Tubulin/FtsZ family, GTPase domain Structure of the alphabeta tubulin dimer by electron family 2, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution index pos1 pos2 score npdbs avgdist mindist nshort 0 205 343 12.450261 0 - - 0 299 PF01175 PF02881 79 1 12.437216 family 1, PF01175: Urocanase family 2, PF02881: SRP54-type protein, helical bundle domain Crystal structure of the NG domain from the index pos1 pos2 score npdbs avgdist mindist nshort 0 820 93 12.437217 0 - - 0 #300 PF00490 PF05683 82 1 12.384667 family 1, PF00490: Delta-aminolevulinic acid dehydratase family 2, PF05683: Fumarase C-terminus Oxygen- and growth rate-dependent regulation of Escherichia index pos1 pos2 score npdbs avgdist mindist nshort 0 143 228 12.384668 0 - - 0 301 PF00471 PF02091 124 1 12.357058 family 1, PF00471: Ribosomal protein L33 family 2, PF02091: Glycyl-tRNA synthetase alpha subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 53 271 12.357059 0 - - 0 302 PF04560 PF06418 231 1 12.342650 family 1, PF04560: RNA polymerase Rpb2, domain 7 Structural basis of transcription: RNA polymerase II at 2.8 family 2, PF06418: CTP synthase N-terminus Thr-431 and Arg-433 are part of a conserved sequence motif index pos1 pos2 score npdbs avgdist mindist nshort 0 66 395 12.342651 0 - - 0 303 PF00163 PF04998 268 1 12.302453 family 1, PF00163: Ribosomal protein S4/S9 N-terminal domain The crystal structure of ribosomal protein S4 reveals a family 2, PF04998: RNA polymerase Rpb1, domain 5 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 87 11 12.302454 0 - - 0 304 PF00471 PF02401 147 1 12.295517 family 1, PF00471: Ribosomal protein L33 family 2, PF02401: LytB protein Identification of the Escherichia coli lytB gene, which is index pos1 pos2 score npdbs avgdist mindist nshort 0 53 453 12.295518 0 - - 0 305 PF01197 PF02556 67 1 12.270019 family 1, PF01197: Ribosomal protein L31 family 2, PF02556: Preprotein translocase subunit SecB Characterization of the Escherichia coli protein-export index pos1 pos2 score npdbs avgdist mindist nshort 0 30 237 12.270019 0 - - 0 306 PF01702 PF02657 70 1 12.264915 family 1, PF01702: Queuine tRNA-ribosyltransferase Crystal structure of tRNA-guanine transglycosylase: RNA family 2, PF02657: Fe-S metabolism associated domain SoxR-dependent response to oxidative stress and virulence index pos1 pos2 score npdbs avgdist mindist nshort 0 548 12 12.264916 0 - - 0 307 PF02882 PF06509 51 1 12.219748 family 1, PF02882: Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain The 3-D structure of a folate-dependent family 2, PF06509: HtpX N-terminus Isolation, characterization, and sequence of an Escherichia index pos1 pos2 score npdbs avgdist mindist nshort 0 392 55 12.219749 0 - - 0 *308 PF00140 PF04545 224 1 12.150086 family 1, PF00140: Sigma-70 factor, region 1.2 Crystal structure of a sigma 70 subunit fragment from E. family 2, PF04545: Sigma-70, region 4 Structure of the bacterial RNA polymerase promoter index pos1 pos2 score npdbs avgdist mindist nshort 0 16 52 12.150087 1 87.7130 87.7130 0 309 PF00438 PF01175 74 1 12.131857 family 1, PF00438: S-adenosylmethionine synthetase, N-terminal domain Structure and function of S-adenosylmethionine synthetase: family 2, PF01175: Urocanase index pos1 pos2 score npdbs avgdist mindist nshort 0 61 820 12.131858 0 - - 0 310 PF00889 PF04285 47 1 12.100056 family 1, PF00889: Elongation factor TS family 2, PF04285: Protein of unknown function (DUF444) index pos1 pos2 score npdbs avgdist mindist nshort 0 558 276 12.100056 0 - - 0 311 PF01316 PF02767 85 1 12.009240 family 1, PF01316: Arginine repressor, DNA binding domain Solution structure of the DNA-binding domain and model for family 2, PF02767: DNA polymerase III beta subunit, central domain Three-dimensional structure of the beta subunit of E. coli index pos1 pos2 score npdbs avgdist mindist nshort 0 46 41 12.009241 0 - - 0 312 PF01175 PF06968 58 1 11.987868 family 1, PF01175: Urocanase family 2, PF06968: Biotin and Thiamin Synthesis associated domain The PLP-dependent biotin synthase from Escherichia coli: index pos1 pos2 score npdbs avgdist mindist nshort 0 669 50 11.987869 0 - - 0 313 PF00342 PF05191 119 1 11.959232 family 1, PF00342: Phosphoglucose isomerase Crystallographic structure analysis of glucose 6-phosphate family 2, PF05191: Adenylate kinase, active site lid Crystal structures of Bacillus stearothermophilus adenylate index pos1 pos2 score npdbs avgdist mindist nshort 0 301 44 11.959232 0 - - 0 314 PF01175 PF04560 78 1 11.878930 family 1, PF01175: Urocanase family 2, PF04560: RNA polymerase Rpb2, domain 7 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 820 218 11.878931 0 - - 0 315 PF00218 PF03918 48 1 11.845893 family 1, PF00218: Indole-3-glycerol phosphate synthase family 2, PF03918: Cytochrome C biogenesis protein Characterization of the Escherichia coli CcmH protein index pos1 pos2 score npdbs avgdist mindist nshort 0 17 137 11.845894 0 - - 0 316 PF03588 PF05188 70 1 11.845206 family 1, PF03588: Leucyl/phenylalanyl-tRNA protein transferase family 2, PF05188: MutS domain II Domain organization and functional analysis of Thermus index pos1 pos2 score npdbs avgdist mindist nshort 0 16 315 11.845207 0 - - 0 317 PF00318 PF04565 295 1 11.841219 family 1, PF00318: Ribosomal protein S2 family 2, PF04565: RNA polymerase Rpb2, domain 3 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 378 49 11.841221 0 - - 0 318 PF01964 PF04359 48 1 11.786510 family 1, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes family 2, PF04359: Protein of unknown function (DUF493) index pos1 pos2 score npdbs avgdist mindist nshort 0 326 18 11.786511 0 - - 0 319 PF00742 PF02153 144 1 11.779856 family 1, PF00742: Homoserine dehydrogenase family 2, PF02153: Prephenate dehydrogenase index pos1 pos2 score npdbs avgdist mindist nshort 0 89 489 11.779857 0 - - 0 320 PF00318 PF01790 181 1 11.734000 family 1, PF00318: Ribosomal protein S2 family 2, PF01790: Prolipoprotein diacylglyceryl transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 40 191 11.734001 0 - - 0 321 PF06026 PF06725 68 1 11.716067 family 1, PF06026: Ribose 5-phosphate isomerase A (phosphoriboisomerase A) Crystal structure of D-ribose-5-phosphate isomerase (RpiA) family 2, PF06725: 3D domain index pos1 pos2 score npdbs avgdist mindist nshort 0 79 87 11.716067 0 - - 0 322 PF00490 PF02572 85 1 11.711342 family 1, PF00490: Delta-aminolevulinic acid dehydratase family 2, PF02572: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP Cobalamin (vitamin B12) biosynthesis: identification and index pos1 pos2 score npdbs avgdist mindist nshort 0 143 25 11.711342 0 - - 0 323 PF02666 PF02742 49 1 11.676939 family 1, PF02666: Phosphatidylserine decarboxylase Cloning, sequencing, and disruption of the Bacillus family 2, PF02742: Iron dependent repressor, metal binding and dimerisation domain Structures of the apo- and the metal ion-activated forms of index pos1 pos2 score npdbs avgdist mindist nshort 0 1062 38 11.676940 0 - - 0 324 PF01316 PF01807 81 1 11.650300 family 1, PF01316: Arginine repressor, DNA binding domain Solution structure of the DNA-binding domain and model for family 2, PF01807: CHC2 zinc finger Structure of the zinc-binding domain of Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 46 78 11.650301 0 - - 0 325 PF01175 PF01245 71 1 11.642486 family 1, PF01175: Urocanase family 2, PF01245: Ribosomal protein L19 index pos1 pos2 score npdbs avgdist mindist nshort 0 820 76 11.642487 0 - - 0 326 PF02503 PF03331 77 1 11.599106 family 1, PF02503: Polyphosphate kinase Transcription of ppk from Acinetobacter sp. strain ADP1, family 2, PF03331: UDP-3-O-acyl N-acetylglycosamine deacetylase Antibacterial agents that target lipid A biosynthesis in index pos1 pos2 score npdbs avgdist mindist nshort 0 144 221 11.599107 0 - - 0 327 PF00311 PF02092 67 1 11.511146 family 1, PF00311: Phosphoenolpyruvate carboxylase family 2, PF02092: Glycyl-tRNA synthetase beta subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 482 89 11.511147 0 - - 0 328 PF01175 PF08529 66 1 11.450273 family 1, PF01175: Urocanase family 2, PF08529: NusA N-terminal domain An extended RNA binding surface through arrayed S1 and KH index pos1 pos2 score npdbs avgdist mindist nshort 0 820 67 11.450274 0 - - 0 #329 PF02075 PF04608 73 1 11.440167 family 1, PF02075: Crossover junction endodeoxyribonuclease RuvC family 2, PF04608: Phosphatidylglycerophosphatase A The pgpA and pgpB genes of Escherichia coli are not index pos1 pos2 score npdbs avgdist mindist nshort 0 175 7 11.440168 0 - - 0 330 PF00290 PF02091 101 1 11.434794 family 1, PF00290: Tryptophan synthase alpha chain Three-dimensional structure of the tryptophan synthase family 2, PF02091: Glycyl-tRNA synthetase alpha subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 262 45 11.434794 0 - - 0 331 PF02618 PF05195 60 1 11.403249 family 1, PF02618: Aminodeoxychorismate lyase Stereochemistry of the transamination reaction catalyzed by family 2, PF05195: Aminopeptidase P, N-terminal domain Structure and mechanism of a proline-specific index pos1 pos2 score npdbs avgdist mindist nshort 0 288 129 11.403250 0 - - 0 332 PF02401 PF02446 81 1 11.380483 family 1, PF02401: LytB protein Identification of the Escherichia coli lytB gene, which is family 2, PF02446: 4-alpha-glucanotransferase Disproportionating enzyme (4-alpha-glucanotransferase; EC index pos1 pos2 score npdbs avgdist mindist nshort 0 409 529 11.380483 0 - - 0 333 PF02556 PF04093 46 1 11.367892 family 1, PF02556: Preprotein translocase subunit SecB Characterization of the Escherichia coli protein-export family 2, PF04093: rod shape-determining protein MreD index pos1 pos2 score npdbs avgdist mindist nshort 0 252 118 11.367892 0 - - 0 334 PF01784 PF03279 77 1 11.351453 family 1, PF01784: NIF3 (NGG1p interacting factor 3) Transcriptional activation by yeast PDR1p is inhibited by family 2, PF03279: Bacterial lipid A biosynthesis acyltransferase index pos1 pos2 score npdbs avgdist mindist nshort 0 572 165 11.351454 0 - - 0 335 PF00573 PF01264 187 1 11.347713 family 1, PF00573: Ribosomal protein L4/L1 family Yeast ribosomal proteins L4, L17, L20, and L25 exhibit family 2, PF01264: Chorismate synthase index pos1 pos2 score npdbs avgdist mindist nshort 0 162 217 11.347714 0 - - 0 336 PF01351 PF02624 52 1 11.322077 family 1, PF01351: Ribonuclease HII Comparative sequence analysis of ribonucleases HII, III, II family 2, PF02624: YcaO-like family index pos1 pos2 score npdbs avgdist mindist nshort 0 309 189 11.322078 0 - - 0 337 PF01964 PF02684 80 1 11.291887 family 1, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes family 2, PF02684: Lipid-A-disaccharide synthetase Cloning and expression of genes encoding lipid A index pos1 pos2 score npdbs avgdist mindist nshort 0 306 12 11.291888 0 - - 0 338 PF00344 PF04293 51 1 11.240525 family 1, PF00344: eubacterial secY protein family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 1054 296 11.240525 0 - - 0 #339 PF02620 PF06325 103 1 11.230920 family 1, PF02620: Uncharacterized ACR, COG1399 family 2, PF06325: Ribosomal protein L11 methyltransferase (PrmA) Cotranscription of two genes necessary for ribosomal index pos1 pos2 score npdbs avgdist mindist nshort 0 292 583 11.230921 0 - - 0 340 PF01175 PF01510 59 1 11.170075 family 1, PF01175: Urocanase family 2, PF01510: N-acetylmuramoyl-L-alanine amidase Cloning, sequencing and expression of a Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 820 169 11.170076 0 - - 0 #341 PF00164 PF00416 297 1 11.164826 family 1, PF00164: Ribosomal protein S12 family 2, PF00416: Ribosomal protein S13/S18 index pos1 pos2 score npdbs avgdist mindist nshort 0 204 215 11.164828 1 84.1953 84.1953 0 342 PF03746 PF03764 81 1 11.149115 family 1, PF03746: LamB/YcsF family Molecular characterization of the lam locus and sequences family 2, PF03764: Elongation factor G, domain IV index pos1 pos2 score npdbs avgdist mindist nshort 0 78 193 11.149116 0 - - 0 343 PF02390 PF04751 48 1 11.137732 family 1, PF02390: Putative methyltransferase family 2, PF04751: Protein of unknown function (DUF615) index pos1 pos2 score npdbs avgdist mindist nshort 0 126 100 11.137733 0 - - 0 344 PF01450 PF04377 64 1 11.100591 family 1, PF01450: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid family 2, PF04377: Arginine-tRNA-protein transferase, C terminus Alternative splicing results in differential expression, index pos1 pos2 score npdbs avgdist mindist nshort 0 314 253 11.100592 0 - - 0 #345 PF05191 PF08267 82 1 11.083210 family 1, PF05191: Adenylate kinase, active site lid Crystal structures of Bacillus stearothermophilus adenylate family 2, PF08267: Cobalamin-independent synthase, N-terminal domain Crystal structures of cobalamin-independent methionine index pos1 pos2 score npdbs avgdist mindist nshort 0 47 231 11.083211 0 - - 0 346 PF00177 PF06418 235 1 11.056226 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF06418: CTP synthase N-terminus Thr-431 and Arg-433 are part of a conserved sequence motif index pos1 pos2 score npdbs avgdist mindist nshort 0 25 395 11.056227 0 - - 0 #347 PF02302 PF02378 69 1 11.031947 family 1, PF02302: PTS system, Lactose/Cellobiose specific IIB subunit The NMR side-chain assignments and solution structure of family 2, PF02378: Phosphotransferase system, EIIC Novel phosphotransferase system genes revealed by bacterial index pos1 pos2 score npdbs avgdist mindist nshort 0 6 1103 11.031948 0 - - 0 #348 PF00420 PF01058 169 1 10.979454 family 1, PF00420: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L family 2, PF01058: NADH ubiquinone oxidoreductase, 20 Kd subunit The NADH:ubiquinone oxidoreductase (complex I) of index pos1 pos2 score npdbs avgdist mindist nshort 0 40 335 10.979455 0 - - 0 349 PF00488 PF04608 69 1 10.946792 family 1, PF00488: MutS domain V Domain organization and functional analysis of Thermus family 2, PF04608: Phosphatidylglycerophosphatase A The pgpA and pgpB genes of Escherichia coli are not index pos1 pos2 score npdbs avgdist mindist nshort 0 792 7 10.946792 0 - - 0 350 PF01208 PF02446 74 1 10.937490 family 1, PF01208: Uroporphyrinogen decarboxylase (URO-D) family 2, PF02446: 4-alpha-glucanotransferase Disproportionating enzyme (4-alpha-glucanotransferase; EC index pos1 pos2 score npdbs avgdist mindist nshort 0 158 529 10.937491 0 - - 0 351 PF00762 PF02618 119 1 10.932813 family 1, PF00762: Ferrochelatase family 2, PF02618: Aminodeoxychorismate lyase Stereochemistry of the transamination reaction catalyzed by index pos1 pos2 score npdbs avgdist mindist nshort 0 96 318 10.932815 0 - - 0 352 PF01411 PF04293 52 1 10.906295 family 1, PF01411: tRNA synthetases class II (A) family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 368 369 10.906296 0 - - 0 #353 PF02572 PF06574 80 1 10.899493 family 1, PF02572: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP Cobalamin (vitamin B12) biosynthesis: identification and family 2, PF06574: FAD synthetase Purification and characterization of FAD synthetase from index pos1 pos2 score npdbs avgdist mindist nshort 0 162 59 10.899494 0 - - 0 354 PF01855 PF02775 95 1 10.892344 family 1, PF01855: Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-binding domain Molecular and phylogenetic characterization of pyruvate and family 2, PF02775: Thiamine pyrophosphate enzyme, C-terminal TPP binding domain Crystal structure of the thiamin diphosphate-dependent index pos1 pos2 score npdbs avgdist mindist nshort 0 118 191 10.892344 1 13.2217 13.2217 0 355 PF02657 PF05000 77 1 10.849975 family 1, PF02657: Fe-S metabolism associated domain SoxR-dependent response to oxidative stress and virulence family 2, PF05000: RNA polymerase Rpb1, domain 4 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 12 41 10.849977 0 - - 0 356 PF00490 PF08299 141 1 10.845611 family 1, PF00490: Delta-aminolevulinic acid dehydratase family 2, PF08299: Bacterial dnaA protein helix-turn-helix domain index pos1 pos2 score npdbs avgdist mindist nshort 0 151 44 10.845611 0 - - 0 357 PF02867 PF04209 53 1 10.842193 family 1, PF02867: Ribonucleotide reductase, barrel domain Structure of ribonucleotide reductase protein R1. family 2, PF04209: homogentisate 1,2-dioxygenase Crystal structure of human homogentisate dioxygenase. index pos1 pos2 score npdbs avgdist mindist nshort 0 338 228 10.842193 0 - - 0 358 PF00478 PF04362 52 1 10.798527 family 1, PF00478: IMP dehydrogenase / GMP reductase domain Crystal structure of Tritrichomonas foetus family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 357 20 10.798529 0 - - 0 #359 PF01379 PF03588 80 1 10.791815 family 1, PF01379: Porphobilinogen deaminase, dipyromethane cofactor binding domain family 2, PF03588: Leucyl/phenylalanyl-tRNA protein transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 13 37 10.791816 0 - - 0 360 PF00670 PF03186 71 1 10.789833 family 1, PF00670: S-adenosyl-L-homocysteine hydrolase, NAD binding domain family 2, PF03186: CobD/Cbib protein Identification and sequence analysis of genes involved in index pos1 pos2 score npdbs avgdist mindist nshort 0 66 329 10.789834 0 - - 0 361 PF01553 PF04362 51 1 10.762761 family 1, PF01553: Acyltransferase Barth syndrome may be due to an acyltransferase deficiency. family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 118 20 10.762762 0 - - 0 #362 PF00163 PF00203 280 1 10.760756 family 1, PF00163: Ribosomal protein S4/S9 N-terminal domain The crystal structure of ribosomal protein S4 reveals a family 2, PF00203: Ribosomal protein S19 index pos1 pos2 score npdbs avgdist mindist nshort 0 132 77 10.760757 1 105.8266 105.8266 0 363 PF01702 PF01977 111 1 10.709203 family 1, PF01702: Queuine tRNA-ribosyltransferase Crystal structure of tRNA-guanine transglycosylase: RNA family 2, PF01977: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Membrane-associated reactions in ubiquinone biosynthesis in index pos1 pos2 score npdbs avgdist mindist nshort 0 36 568 10.709204 0 - - 0 364 PF01218 PF02578 70 1 10.706252 family 1, PF01218: Coproporphyrinogen III oxidase family 2, PF02578: Uncharacterised ACR, YfiH family COG1496 index pos1 pos2 score npdbs avgdist mindist nshort 0 606 540 10.706253 0 - - 0 *365 PF00206 PF08328 78 1 10.705597 family 1, PF00206: Lyase family 2, PF08328: Adenylosuccinate lyase C-terminal Characterization of the cDNA and the gene encoding murine index pos1 pos2 score npdbs avgdist mindist nshort 0 557 2 10.705597 0 - - 0 366 PF00436 PF01458 120 1 10.705271 family 1, PF00436: Single-strand binding protein family Crystal structure of the homo-tetrameric DNA binding domain family 2, PF01458: Uncharacterized protein family (UPF0051) index pos1 pos2 score npdbs avgdist mindist nshort 0 106 176 10.705272 0 - - 0 #367 PF00347 PF00411 277 1 10.704779 family 1, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene family 2, PF00411: Ribosomal protein S11 index pos1 pos2 score npdbs avgdist mindist nshort 0 179 99 10.704781 0 - - 0 368 PF00662 PF07219 57 1 10.694840 family 1, PF00662: NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus The NADH:ubiquinone oxidoreductase (complex I) of family 2, PF07219: HemY protein N-terminus Bacillus subtilis HemY is a peripheral membrane protein index pos1 pos2 score npdbs avgdist mindist nshort 0 79 86 10.694842 0 - - 0 *369 PF00732 PF05199 130 1 10.683750 family 1, PF00732: GMC oxidoreductase family 2, PF05199: GMC oxidoreductase index pos1 pos2 score npdbs avgdist mindist nshort 0 1305 450 10.683750 3 2.5809 2.4416 3 370 PF01170 PF02568 81 1 10.656447 family 1, PF01170: Putative RNA methylase family UPF0020 THUMP - a predicted RNA-binding domain shared by family 2, PF02568: Thiamine biosynthesis protein (ThiI) Characterization of thiI, a new gene involved in thiazole index pos1 pos2 score npdbs avgdist mindist nshort 0 3 91 10.656447 0 - - 0 371 PF00453 PF01175 71 1 10.650205 family 1, PF00453: Ribosomal protein L20 family 2, PF01175: Urocanase index pos1 pos2 score npdbs avgdist mindist nshort 0 21 820 10.650206 0 - - 0 372 PF02787 PF04379 68 1 10.636323 family 1, PF02787: Carbamoyl-phosphate synthetase large chain, oligomerisation domain The structure of carbamoyl phosphate synthetase determined family 2, PF04379: Protein of unknown function (DUF525) A family of mammalian F-box proteins. index pos1 pos2 score npdbs avgdist mindist nshort 0 123 97 10.636323 0 - - 0 373 PF00162 PF01264 190 1 10.635371 family 1, PF00162: Phosphoglycerate kinase family 2, PF01264: Chorismate synthase index pos1 pos2 score npdbs avgdist mindist nshort 0 485 207 10.635372 0 - - 0 374 PF00278 PF00285 178 1 10.626848 family 1, PF00278: Pyridoxal-dependent decarboxylase, C-terminal sheet domain Structure of mammalian ornithine decarboxylase at 1.6 A family 2, PF00285: Citrate synthase index pos1 pos2 score npdbs avgdist mindist nshort 0 302 750 10.626849 0 - - 0 375 PF00177 PF00285 194 1 10.611382 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF00285: Citrate synthase index pos1 pos2 score npdbs avgdist mindist nshort 0 343 750 10.611383 0 - - 0 376 PF00316 PF01450 85 1 10.572935 family 1, PF00316: Fructose-1-6-bisphosphatase Structure of rabbit liver fructose 1,6-bisphosphatase at family 2, PF01450: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid index pos1 pos2 score npdbs avgdist mindist nshort 0 435 314 10.572936 0 - - 0 377 PF01134 PF01430 118 1 10.565248 family 1, PF01134: Glucose inhibited division protein A family 2, PF01430: Hsp33 protein Chaperone activity with a redox switch. index pos1 pos2 score npdbs avgdist mindist nshort 0 601 24 10.565248 0 - - 0 378 PF00478 PF04376 76 1 10.560633 family 1, PF00478: IMP dehydrogenase / GMP reductase domain Crystal structure of Tritrichomonas foetus family 2, PF04376: Arginine-tRNA-protein transferase, N terminus Alternative splicing results in differential expression, index pos1 pos2 score npdbs avgdist mindist nshort 0 872 124 10.560634 0 - - 0 379 PF03588 PF06071 83 1 10.551685 family 1, PF03588: Leucyl/phenylalanyl-tRNA protein transferase family 2, PF06071: Protein of unknown function (DUF933) index pos1 pos2 score npdbs avgdist mindist nshort 0 16 8 10.551687 0 - - 0 380 PF02113 PF03788 49 1 10.517904 family 1, PF02113: D-Ala-D-Ala carboxypeptidase 3 (S13) family family 2, PF03788: LrgA family Identification of LytSR-regulated genes from Staphylococcus index pos1 pos2 score npdbs avgdist mindist nshort 0 253 34 10.517905 0 - - 0 381 PF01293 PF03486 53 1 10.501596 family 1, PF01293: Phosphoenolpyruvate carboxykinase Snapshot of an enzyme reaction intermediate in the family 2, PF03486: HI0933-like protein index pos1 pos2 score npdbs avgdist mindist nshort 0 179 261 10.501597 0 - - 0 #382 PF03588 PF04997 83 1 10.485970 family 1, PF03588: Leucyl/phenylalanyl-tRNA protein transferase family 2, PF04997: RNA polymerase Rpb1, domain 1 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 16 1214 10.485971 0 - - 0 #383 PF04566 PF04997 250 1 10.453648 family 1, PF04566: RNA polymerase Rpb2, domain 4 Structural basis of transcription: RNA polymerase II at 2.8 family 2, PF04997: RNA polymerase Rpb1, domain 1 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 5 366 10.453649 1 55.4017 55.4017 0 384 PF00562 PF04362 51 1 10.413527 family 1, PF00562: RNA polymerase Rpb2, domain 6 Structural basis of transcription: RNA polymerase II at 2.8 family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 840 53 10.413529 0 - - 0 385 PF00935 PF02516 50 1 10.399858 family 1, PF00935: Ribosomal protein L44 family 2, PF02516: Oligosaccharyl transferase STT3 subunit Molecular cloning of a highly conserved mouse and human index pos1 pos2 score npdbs avgdist mindist nshort 0 38 1428 10.399859 0 - - 0 386 PF04355 PF04546 62 1 10.397380 family 1, PF04355: SmpA / OmlA family Pseudomonas aeruginosa fur overlaps with a gene encoding a family 2, PF04546: Sigma-70, non-essential region Structure of the bacterial RNA polymerase promoter index pos1 pos2 score npdbs avgdist mindist nshort 0 79 465 10.397381 0 - - 0 387 PF00342 PF02091 117 1 10.396456 family 1, PF00342: Phosphoglucose isomerase Crystallographic structure analysis of glucose 6-phosphate family 2, PF02091: Glycyl-tRNA synthetase alpha subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 527 45 10.396458 0 - - 0 #388 PF00189 PF00237 324 1 10.378439 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF00237: Ribosomal protein L22p/L17e The crystal structure of ribosomal protein L22 from Thermus index pos1 pos2 score npdbs avgdist mindist nshort 0 132 262 10.378440 0 - - 0 389 PF01293 PF07733 65 1 10.360749 family 1, PF01293: Phosphoenolpyruvate carboxykinase Snapshot of an enzyme reaction intermediate in the family 2, PF07733: Bacterial DNA polymerase III alpha subunit Phosphoesterase domains associated with DNA polymerases of index pos1 pos2 score npdbs avgdist mindist nshort 0 179 572 10.360750 0 - - 0 390 PF01964 PF08494 47 1 10.331517 family 1, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes family 2, PF08494: DEAD/H associated index pos1 pos2 score npdbs avgdist mindist nshort 0 252 26 10.331518 0 - - 0 391 PF07991 PF08212 46 1 10.315100 family 1, PF07991: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid family 2, PF08212: Lipocalin-like domain index pos1 pos2 score npdbs avgdist mindist nshort 0 161 60 10.315101 0 - - 0 392 PF01743 PF01985 86 1 10.284900 family 1, PF01743: Poly A polymerase family Identification of the gene for an Escherichia coli poly(A) family 2, PF01985: CRS1 / YhbY domain Crystal structure of E. coli YhbY: a representative of a index pos1 pos2 score npdbs avgdist mindist nshort 0 311 61 10.284901 0 - - 0 393 PF02657 PF02768 72 1 10.280163 family 1, PF02657: Fe-S metabolism associated domain SoxR-dependent response to oxidative stress and virulence family 2, PF02768: DNA polymerase III beta subunit, C-terminal domain Three-dimensional structure of the beta subunit of E. coli index pos1 pos2 score npdbs avgdist mindist nshort 0 12 87 10.280164 0 - - 0 394 PF00276 PF04285 49 1 10.271713 family 1, PF00276: Ribosomal protein L23 family 2, PF04285: Protein of unknown function (DUF444) index pos1 pos2 score npdbs avgdist mindist nshort 0 0 276 10.271714 0 - - 0 395 PF01175 PF02580 64 1 10.267131 family 1, PF01175: Urocanase family 2, PF02580: D-Tyr-tRNA(Tyr) deacylase Structure of crystalline D-Tyr-tRNA(Tyr) deacylase. A index pos1 pos2 score npdbs avgdist mindist nshort 0 820 129 10.267132 0 - - 0 396 PF00800 PF04751 51 1 10.248484 family 1, PF00800: Prephenate dehydratase family 2, PF04751: Protein of unknown function (DUF615) index pos1 pos2 score npdbs avgdist mindist nshort 0 66 191 10.248485 0 - - 0 *397 PF00767 PF08440 50 1 10.230212 family 1, PF00767: Potyvirus coat protein family 2, PF08440: Potyviridae polyprotein index pos1 pos2 score npdbs avgdist mindist nshort 0 83 189 10.230213 0 - - 0 398 PF00410 PF04997 241 1 10.226846 family 1, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein family 2, PF04997: RNA polymerase Rpb1, domain 1 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 262 24 10.226847 0 - - 0 399 PF01619 PF08529 108 1 10.226696 family 1, PF01619: Proline dehydrogenase Sequence analysis identifies the proline dehydrogenase and family 2, PF08529: NusA N-terminal domain An extended RNA binding surface through arrayed S1 and KH index pos1 pos2 score npdbs avgdist mindist nshort 0 927 81 10.226697 0 - - 0 400 PF01784 PF02965 77 1 10.221250 family 1, PF01784: NIF3 (NGG1p interacting factor 3) Transcriptional activation by yeast PDR1p is inhibited by family 2, PF02965: Vitamin B12 dependent methionine synthase, activation domain The structure of the C-terminal domain of methionine index pos1 pos2 score npdbs avgdist mindist nshort 0 710 110 10.221251 0 - - 0 401 PF02606 PF03922 51 1 10.214107 family 1, PF02606: Tetraacyldisaccharide-1-P 4'-kinase Accumulation of a lipid A precursor lacking the family 2, PF03922: OmpW family Characterization of colicin S4 and its receptor, OmpW, a index pos1 pos2 score npdbs avgdist mindist nshort 0 103 492 10.214107 0 - - 0 402 PF01783 PF01977 92 1 10.209846 family 1, PF01783: Ribosomal L32p protein family family 2, PF01977: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Membrane-associated reactions in ubiquinone biosynthesis in index pos1 pos2 score npdbs avgdist mindist nshort 0 14 627 10.209846 0 - - 0 403 PF00816 PF02542 46 1 10.209581 family 1, PF00816: H-NS histone family Solution structure of the DNA binding domain of a family 2, PF02542: YgbB family Biosynthesis of terpenoids: YgbB protein converts index pos1 pos2 score npdbs avgdist mindist nshort 0 157 222 10.209583 0 - - 0 404 PF02866 PF04546 57 1 10.202361 family 1, PF02866: lactate/malate dehydrogenase, alpha/beta C-terminal domain Structural basis of substrate specificity in malate family 2, PF04546: Sigma-70, non-essential region Structure of the bacterial RNA polymerase promoter index pos1 pos2 score npdbs avgdist mindist nshort 0 71 363 10.202362 0 - - 0 405 PF01175 PF07479 72 1 10.198525 family 1, PF01175: Urocanase family 2, PF07479: NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus Kinetic regulation of the mitochondrial index pos1 pos2 score npdbs avgdist mindist nshort 0 820 67 10.198525 0 - - 0 #406 PF00316 PF02446 51 1 10.191745 family 1, PF00316: Fructose-1-6-bisphosphatase Structure of rabbit liver fructose 1,6-bisphosphatase at family 2, PF02446: 4-alpha-glucanotransferase Disproportionating enzyme (4-alpha-glucanotransferase; EC index pos1 pos2 score npdbs avgdist mindist nshort 0 113 982 10.191746 0 - - 0 407 PF00338 PF03588 82 1 10.189624 family 1, PF00338: Ribosomal protein S10p/S20e family 2, PF03588: Leucyl/phenylalanyl-tRNA protein transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 62 16 10.189624 0 - - 0 408 PF03548 PF04359 52 1 10.182799 family 1, PF03548: Outer membrane lipoprotein carrier protein LolA family 2, PF04359: Protein of unknown function (DUF493) index pos1 pos2 score npdbs avgdist mindist nshort 0 153 18 10.182799 0 - - 0 409 PF00334 PF01175 75 1 10.176238 family 1, PF00334: Nucleoside diphosphate kinase family 2, PF01175: Urocanase index pos1 pos2 score npdbs avgdist mindist nshort 0 80 820 10.176239 0 - - 0 410 PF00311 PF00977 82 1 10.169347 family 1, PF00311: Phosphoenolpyruvate carboxylase family 2, PF00977: Histidine biosynthesis protein Paralogous histidine biosynthetic genes: evolutionary index pos1 pos2 score npdbs avgdist mindist nshort 0 2152 174 10.169348 0 - - 0 *411 PF00749 PF03950 140 1 10.167725 family 1, PF00749: tRNA synthetases class I (E and Q), catalytic domain How glutaminyl-tRNA synthetase selects glutamine. family 2, PF03950: tRNA synthetases class I (E and Q), anti-codon binding domain How glutaminyl-tRNA synthetase selects glutamine. index pos1 pos2 score npdbs avgdist mindist nshort 0 26 132 10.167726 1 48.6288 48.6288 0 412 PF01985 PF02390 82 1 10.157410 family 1, PF01985: CRS1 / YhbY domain Crystal structure of E. coli YhbY: a representative of a family 2, PF02390: Putative methyltransferase index pos1 pos2 score npdbs avgdist mindist nshort 0 61 118 10.157411 0 - - 0 413 PF02938 PF03588 77 1 10.157281 family 1, PF02938: GAD domain family 2, PF03588: Leucyl/phenylalanyl-tRNA protein transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 150 16 10.157282 0 - - 0 414 PF00867 PF03031 46 1 10.137349 family 1, PF00867: XPG I-region Flap endonuclease homologs in archaebacteria exist as family 2, PF03031: NLI interacting factor-like phosphatase Defining the active site of Schizosaccharomyces pombe CTD index pos1 pos2 score npdbs avgdist mindist nshort 0 69 283 10.137351 0 - - 0 415 PF00490 PF02660 108 1 10.133693 family 1, PF00490: Delta-aminolevulinic acid dehydratase family 2, PF02660: Domain of unknown function DUF index pos1 pos2 score npdbs avgdist mindist nshort 0 387 493 10.133693 0 - - 0 416 PF00344 PF06418 234 1 10.126846 family 1, PF00344: eubacterial secY protein family 2, PF06418: CTP synthase N-terminus Thr-431 and Arg-433 are part of a conserved sequence motif index pos1 pos2 score npdbs avgdist mindist nshort 0 1177 395 10.126847 0 - - 0 #417 PF00312 PF00687 225 1 10.125235 family 1, PF00312: Ribosomal protein S15 Conformational variability of the N-terminal helix in the family 2, PF00687: Ribosomal protein L1p/L10e family index pos1 pos2 score npdbs avgdist mindist nshort 0 33 547 10.125236 0 - - 0 418 PF00749 PF02036 65 1 10.121870 family 1, PF00749: tRNA synthetases class I (E and Q), catalytic domain How glutaminyl-tRNA synthetase selects glutamine. family 2, PF02036: SCP-2 sterol transfer family NMR determination of the secondary structure and the index pos1 pos2 score npdbs avgdist mindist nshort 0 738 114 10.121871 0 - - 0 419 PF00827 PF05191 47 1 10.114818 family 1, PF00827: Ribosomal L15 family 2, PF05191: Adenylate kinase, active site lid Crystal structures of Bacillus stearothermophilus adenylate index pos1 pos2 score npdbs avgdist mindist nshort 0 96 1 10.114819 0 - - 0 420 PF00152 PF04381 47 1 10.104732 family 1, PF00152: tRNA synthetases class II (D, K and N) family 2, PF04381: Putative exonuclease, RdgC A homologue of the recombination-dependent growth gene, index pos1 pos2 score npdbs avgdist mindist nshort 0 922 140 10.104733 0 - - 0 421 PF00762 PF03205 65 1 10.097447 family 1, PF00762: Ferrochelatase family 2, PF03205: Molybdopterin guanine dinucleotide synthesis protein B index pos1 pos2 score npdbs avgdist mindist nshort 0 205 40 10.097448 0 - - 0 #422 PF00318 PF00347 229 1 10.088037 family 1, PF00318: Ribosomal protein S2 family 2, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene index pos1 pos2 score npdbs avgdist mindist nshort 0 20 174 10.088037 0 - - 0 423 PF00453 PF03550 52 1 10.068080 family 1, PF00453: Ribosomal protein L20 family 2, PF03550: Outer membrane lipoprotein LolB index pos1 pos2 score npdbs avgdist mindist nshort 0 41 156 10.068080 0 - - 0 424 PF01813 PF02390 54 1 10.062614 family 1, PF01813: ATP synthase subunit D Subunit structure and organization of the genes of the A1A0 family 2, PF02390: Putative methyltransferase index pos1 pos2 score npdbs avgdist mindist nshort 0 207 590 10.062615 0 - - 0 #425 PF00189 PF03947 323 1 10.057206 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF03947: Ribosomal Proteins L2, C-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 132 207 10.057207 0 - - 0 #426 PF00281 PF00347 274 1 10.056588 family 1, PF00281: Ribosomal protein L5 family 2, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene index pos1 pos2 score npdbs avgdist mindist nshort 0 84 179 10.056589 2 110.4116 103.5820 0 427 PF00012 PF08298 51 1 10.054747 family 1, PF00012: Hsp70 protein The Hsp70 and Hsp60 chaperone machines. family 2, PF08298: PrkA AAA domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 2563 264 10.054748 0 - - 0 #428 PF00308 PF01293 61 1 10.036093 family 1, PF00308: Bacterial dnaA protein family 2, PF01293: Phosphoenolpyruvate carboxykinase Snapshot of an enzyme reaction intermediate in the index pos1 pos2 score npdbs avgdist mindist nshort 0 96 179 10.036094 0 - - 0 #429 PF00623 PF04565 289 1 10.030432 family 1, PF00623: RNA polymerase Rpb1, domain 2 Structural modules of the large subunits of RNA polymerase. family 2, PF04565: RNA polymerase Rpb2, domain 3 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 387 49 10.030433 2 47.5628 46.6712 0 430 PF00344 PF03588 83 1 10.012309 family 1, PF00344: eubacterial secY protein family 2, PF03588: Leucyl/phenylalanyl-tRNA protein transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 885 16 10.012309 0 - - 0 431 PF02401 PF02742 60 1 10.011683 family 1, PF02401: LytB protein Identification of the Escherichia coli lytB gene, which is family 2, PF02742: Iron dependent repressor, metal binding and dimerisation domain Structures of the apo- and the metal ion-activated forms of index pos1 pos2 score npdbs avgdist mindist nshort 0 171 38 10.011684 0 - - 0 432 PF01433 PF04362 50 1 10.007816 family 1, PF01433: Peptidase family M1 Evolutionary families of metallopeptidases. family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 1075 20 10.007817 0 - - 0 433 PF02091 PF03737 55 1 10.006359 family 1, PF02091: Glycyl-tRNA synthetase alpha subunit family 2, PF03737: Demethylmenaquinone methyltransferase Identification of a novel gene cluster participating in index pos1 pos2 score npdbs avgdist mindist nshort 0 45 208 10.006360 0 - - 0 434 PF00411 PF00623 239 1 10.001728 family 1, PF00411: Ribosomal protein S11 family 2, PF00623: RNA polymerase Rpb1, domain 2 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 29 130 10.001728 0 - - 0 #435 PF04563 PF05000 273 1 9.987687 family 1, PF04563: RNA polymerase beta subunit RNA polymerase II of Drosophila. Relation of its 140,000 Mr family 2, PF05000: RNA polymerase Rpb1, domain 4 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 1194 19 9.987689 2 53.0502 48.4533 0 436 PF00342 PF06798 51 1 9.964722 family 1, PF00342: Phosphoglucose isomerase Crystallographic structure analysis of glucose 6-phosphate family 2, PF06798: PrkA serine protein kinase C-terminal domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 403 26 9.964723 0 - - 0 437 PF00317 PF03734 81 1 9.958523 family 1, PF00317: Ribonucleotide reductase, all-alpha domain Structure of ribonucleotide reductase protein R1. family 2, PF03734: ErfK/YbiS/YcfS/YnhG index pos1 pos2 score npdbs avgdist mindist nshort 0 177 100 9.958524 0 - - 0 438 PF01991 PF02390 49 1 9.951196 family 1, PF01991: ATP synthase (E/31 kDa) subunit The 31-kDa polypeptide is an essential subunit of the family 2, PF02390: Putative methyltransferase index pos1 pos2 score npdbs avgdist mindist nshort 0 397 590 9.951197 0 - - 0 439 PF01379 PF01992 47 1 9.949693 family 1, PF01379: Porphobilinogen deaminase, dipyromethane cofactor binding domain family 2, PF01992: ATP synthase (C/AC39) subunit The Saccharomyces cerevisiae VMA6 gene encodes the 36-kDa index pos1 pos2 score npdbs avgdist mindist nshort 0 153 123 9.949694 0 - - 0 440 PF00177 PF04998 299 1 9.945064 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF04998: RNA polymerase Rpb1, domain 5 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 97 55 9.945065 0 - - 0 441 PF01790 PF06723 126 1 9.940687 family 1, PF01790: Prolipoprotein diacylglyceryl transferase family 2, PF06723: MreB/Mbl protein Cytoskeletons in prokaryotes. index pos1 pos2 score npdbs avgdist mindist nshort 0 353 184 9.940688 0 - - 0 442 PF00750 PF04381 47 1 9.939584 family 1, PF00750: tRNA synthetases class I (R) family 2, PF04381: Putative exonuclease, RdgC A homologue of the recombination-dependent growth gene, index pos1 pos2 score npdbs avgdist mindist nshort 0 1296 92 9.939585 0 - - 0 443 PF01264 PF04608 62 1 9.934339 family 1, PF01264: Chorismate synthase family 2, PF04608: Phosphatidylglycerophosphatase A The pgpA and pgpB genes of Escherichia coli are not index pos1 pos2 score npdbs avgdist mindist nshort 0 44 7 9.934340 0 - - 0 444 PF00160 PF00762 158 1 9.932993 family 1, PF00160: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD The cyclophilins. family 2, PF00762: Ferrochelatase index pos1 pos2 score npdbs avgdist mindist nshort 0 966 96 9.932994 0 - - 0 445 PF00476 PF04379 71 1 9.931226 family 1, PF00476: DNA polymerase family A family 2, PF04379: Protein of unknown function (DUF525) A family of mammalian F-box proteins. index pos1 pos2 score npdbs avgdist mindist nshort 0 13 97 9.931227 0 - - 0 446 PF00707 PF04997 192 1 9.914598 family 1, PF00707: Translation initiation factor IF-3, C-terminal domain family 2, PF04997: RNA polymerase Rpb1, domain 1 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 10 210 9.914599 0 - - 0 447 PF03717 PF04401 47 1 9.911236 family 1, PF03717: Penicillin-binding Protein dimerisation domain family 2, PF04401: Protein of unknown function (DUF540) index pos1 pos2 score npdbs avgdist mindist nshort 0 222 114 9.911236 0 - - 0 448 PF00189 PF02622 101 1 9.910792 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF02622: Uncharacterized ACR, COG1678 index pos1 pos2 score npdbs avgdist mindist nshort 0 92 150 9.910793 0 - - 0 #449 PF00490 PF00762 169 1 9.910780 family 1, PF00490: Delta-aminolevulinic acid dehydratase family 2, PF00762: Ferrochelatase index pos1 pos2 score npdbs avgdist mindist nshort 0 151 453 9.910782 0 - - 0 450 PF03315 PF03951 109 1 9.893224 family 1, PF03315: Serine dehydratase beta chain family 2, PF03951: Glutamine synthetase, beta-Grasp domain index pos1 pos2 score npdbs avgdist mindist nshort 0 309 5 9.893224 0 - - 0 451 PF02548 PF04952 49 1 9.892744 family 1, PF02548: Ketopantoate hydroxymethyltransferase Cloning and sequencing of the Escherichia coli panB gene, family 2, PF04952: Succinylglutamate desuccinylase / Aspartoacylase family Cloning of the human aspartoacylase cDNA and a common index pos1 pos2 score npdbs avgdist mindist nshort 0 202 594 9.892745 0 - - 0 452 PF00623 PF01351 227 1 9.878533 family 1, PF00623: RNA polymerase Rpb1, domain 2 Structural modules of the large subunits of RNA polymerase. family 2, PF01351: Ribonuclease HII Comparative sequence analysis of ribonucleases HII, III, II index pos1 pos2 score npdbs avgdist mindist nshort 0 395 618 9.878534 0 - - 0 453 PF00572 PF03588 82 1 9.842825 family 1, PF00572: Ribosomal protein L13 family 2, PF03588: Leucyl/phenylalanyl-tRNA protein transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 158 16 9.842825 0 - - 0 454 PF00347 PF04563 256 1 9.837526 family 1, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene family 2, PF04563: RNA polymerase beta subunit RNA polymerase II of Drosophila. Relation of its 140,000 Mr index pos1 pos2 score npdbs avgdist mindist nshort 0 179 1194 9.837527 0 - - 0 455 PF01985 PF02224 85 1 9.836984 family 1, PF01985: CRS1 / YhbY domain Crystal structure of E. coli YhbY: a representative of a family 2, PF02224: Cytidylate kinase Structures of escherichia coli CMP kinase alone and in index pos1 pos2 score npdbs avgdist mindist nshort 0 61 195 9.836985 0 - - 0 456 PF00203 PF01175 79 1 9.835958 family 1, PF00203: Ribosomal protein S19 family 2, PF01175: Urocanase index pos1 pos2 score npdbs avgdist mindist nshort 0 113 820 9.835959 0 - - 0 457 PF02867 PF04359 48 1 9.831910 family 1, PF02867: Ribonucleotide reductase, barrel domain Structure of ribonucleotide reductase protein R1. family 2, PF04359: Protein of unknown function (DUF493) index pos1 pos2 score npdbs avgdist mindist nshort 0 87 18 9.831912 0 - - 0 458 PF02618 PF03331 87 1 9.831033 family 1, PF02618: Aminodeoxychorismate lyase Stereochemistry of the transamination reaction catalyzed by family 2, PF03331: UDP-3-O-acyl N-acetylglycosamine deacetylase Antibacterial agents that target lipid A biosynthesis in index pos1 pos2 score npdbs avgdist mindist nshort 0 288 221 9.831034 0 - - 0 459 PF01977 PF03966 66 1 9.825935 family 1, PF01977: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Membrane-associated reactions in ubiquinone biosynthesis in family 2, PF03966: Trm112p-like protein Trm11p and Trm112p Are both Required for the Formation of index pos1 pos2 score npdbs avgdist mindist nshort 0 748 168 9.825936 0 - - 0 460 PF00297 PF01175 80 1 9.823495 family 1, PF00297: Ribosomal protein L3 family 2, PF01175: Urocanase index pos1 pos2 score npdbs avgdist mindist nshort 0 378 820 9.823496 0 - - 0 461 PF01293 PF01654 57 1 9.822315 family 1, PF01293: Phosphoenolpyruvate carboxykinase Snapshot of an enzyme reaction intermediate in the family 2, PF01654: Bacterial Cytochrome Ubiquinol Oxidase The Klebsiella pneumoniae cytochrome bd' terminal oxidase index pos1 pos2 score npdbs avgdist mindist nshort 0 179 894 9.822316 0 - - 0 462 PF01326 PF04608 63 1 9.805618 family 1, PF01326: Pyruvate phosphate dikinase, PEP/pyruvate binding domain Swiveling-domain mechanism for enzymatic phosphotransfer family 2, PF04608: Phosphatidylglycerophosphatase A The pgpA and pgpB genes of Escherichia coli are not index pos1 pos2 score npdbs avgdist mindist nshort 0 438 7 9.805618 0 - - 0 463 PF00977 PF04209 48 1 9.799985 family 1, PF00977: Histidine biosynthesis protein Paralogous histidine biosynthetic genes: evolutionary family 2, PF04209: homogentisate 1,2-dioxygenase Crystal structure of human homogentisate dioxygenase. index pos1 pos2 score npdbs avgdist mindist nshort 0 546 299 9.799986 0 - - 0 464 PF00285 PF04293 49 1 9.799045 family 1, PF00285: Citrate synthase family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 744 465 9.799045 0 - - 0 465 PF01977 PF03193 66 1 9.798498 family 1, PF01977: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Membrane-associated reactions in ubiquinone biosynthesis in family 2, PF03193: Protein of unknown function, DUF258 index pos1 pos2 score npdbs avgdist mindist nshort 0 766 205 9.798499 0 - - 0 466 PF01783 PF04608 71 1 9.797323 family 1, PF01783: Ribosomal L32p protein family family 2, PF04608: Phosphatidylglycerophosphatase A The pgpA and pgpB genes of Escherichia coli are not index pos1 pos2 score npdbs avgdist mindist nshort 0 29 12 9.797324 0 - - 0 467 PF00731 PF06798 51 1 9.789026 family 1, PF00731: AIR carboxylase Crystal structure of Escherichia coli PurE, an unusual family 2, PF06798: PrkA serine protein kinase C-terminal domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 23 52 9.789026 0 - - 0 468 PF00584 PF08298 47 1 9.788219 family 1, PF00584: SecE/Sec61-gamma subunits of protein translocation complex Protein translocation in the three domains of life: family 2, PF08298: PrkA AAA domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 56 421 9.788220 0 - - 0 469 PF01619 PF02657 54 1 9.779490 family 1, PF01619: Proline dehydrogenase Sequence analysis identifies the proline dehydrogenase and family 2, PF02657: Fe-S metabolism associated domain SoxR-dependent response to oxidative stress and virulence index pos1 pos2 score npdbs avgdist mindist nshort 0 684 12 9.779491 0 - - 0 470 PF04285 PF06798 49 1 9.775867 family 1, PF04285: Protein of unknown function (DUF444) family 2, PF06798: PrkA serine protein kinase C-terminal domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 183 26 9.775868 0 - - 0 #471 PF01541 PF02650 64 1 9.767037 family 1, PF01541: GIY-YIG catalytic domain Identification of a family of bacteriophage T4 genes family 2, PF02650: Uncharacterized BCR, COG1481 index pos1 pos2 score npdbs avgdist mindist nshort 0 8 315 9.767038 0 - - 0 472 PF00238 PF04330 54 1 9.765340 family 1, PF00238: Ribosomal protein L14p/L23e family 2, PF04330: Family of unknown function (DUF471) Staphylococcus aureus resistance to human defensins and index pos1 pos2 score npdbs avgdist mindist nshort 0 6 101 9.765341 0 - - 0 #473 PF01262 PF02233 105 1 9.746931 family 1, PF01262: Alanine dehydrogenase/PNT, C-terminal domain Lysine metabolism in higher plants. family 2, PF02233: NAD(P) transhydrogenase beta subunit A mutation at Gly314 of the beta subunit of the Escherichia index pos1 pos2 score npdbs avgdist mindist nshort 0 9 625 9.746932 0 - - 0 474 PF00670 PF01960 89 1 9.746708 family 1, PF00670: S-adenosyl-L-homocysteine hydrolase, NAD binding domain family 2, PF01960: ArgJ family Primary structure, partial purification and regulation of index pos1 pos2 score npdbs avgdist mindist nshort 0 66 678 9.746709 0 - - 0 475 PF01464 PF03524 58 1 9.742364 family 1, PF01464: Transglycosylase SLT domain A conserved domain in putative bacterial and bacteriophage family 2, PF03524: Conjugal transfer protein index pos1 pos2 score npdbs avgdist mindist nshort 0 407 742 9.742364 0 - - 0 476 PF01641 PF03749 50 1 9.737835 family 1, PF01641: SelR domain Novel selenoproteins identified in silico and in vivo by family 2, PF03749: Sugar fermentation stimulation protein Nucleotide sequence and characterization of the sfs1 gene: index pos1 pos2 score npdbs avgdist mindist nshort 0 64 74 9.737836 0 - - 0 477 PF02785 PF06509 51 1 9.725462 family 1, PF02785: Biotin carboxylase C-terminal domain Three-dimensional structure of the biotin carboxylase family 2, PF06509: HtpX N-terminus Isolation, characterization, and sequence of an Escherichia index pos1 pos2 score npdbs avgdist mindist nshort 0 105 72 9.725462 0 - - 0 #478 PF00410 PF01409 240 1 9.719694 family 1, PF00410: Ribosomal protein S8 Structural evidence for specific S8-RNA and S8-protein family 2, PF01409: tRNA synthetases class II core domain (F) index pos1 pos2 score npdbs avgdist mindist nshort 0 214 750 9.719695 0 - - 0 479 PF00768 PF04285 46 1 9.718957 family 1, PF00768: D-alanyl-D-alanine carboxypeptidase family 2, PF04285: Protein of unknown function (DUF444) index pos1 pos2 score npdbs avgdist mindist nshort 0 551 465 9.718958 0 - - 0 #480 PF00204 PF03950 123 1 9.710430 family 1, PF00204: DNA gyrase B Crystal structure of an N-terminal fragment of the DNA family 2, PF03950: tRNA synthetases class I (E and Q), anti-codon binding domain How glutaminyl-tRNA synthetase selects glutamine. index pos1 pos2 score npdbs avgdist mindist nshort 0 118 163 9.710431 0 - - 0 481 PF00490 PF01813 58 1 9.689561 family 1, PF00490: Delta-aminolevulinic acid dehydratase family 2, PF01813: ATP synthase subunit D Subunit structure and organization of the genes of the A1A0 index pos1 pos2 score npdbs avgdist mindist nshort 0 143 30 9.689562 0 - - 0 482 PF00380 PF03618 99 1 9.686841 family 1, PF00380: Ribosomal protein S9/S16 family 2, PF03618: Domain of unknown function (DUF299) index pos1 pos2 score npdbs avgdist mindist nshort 0 14 285 9.686842 0 - - 0 483 PF01264 PF04377 63 1 9.659658 family 1, PF01264: Chorismate synthase family 2, PF04377: Arginine-tRNA-protein transferase, C terminus Alternative splicing results in differential expression, index pos1 pos2 score npdbs avgdist mindist nshort 0 467 253 9.659659 0 - - 0 484 PF00204 PF01916 57 1 9.658776 family 1, PF00204: DNA gyrase B Crystal structure of an N-terminal fragment of the DNA family 2, PF01916: Deoxyhypusine synthase Crystal structure of the NAD complex of human deoxyhypusine index pos1 pos2 score npdbs avgdist mindist nshort 0 118 659 9.658777 0 - - 0 485 PF03739 PF08328 48 1 9.657729 family 1, PF03739: Predicted permease YjgP/YjgQ family family 2, PF08328: Adenylosuccinate lyase C-terminal Characterization of the cDNA and the gene encoding murine index pos1 pos2 score npdbs avgdist mindist nshort 0 71 92 9.657730 0 - - 0 #486 PF00163 PF00281 252 1 9.654118 family 1, PF00163: Ribosomal protein S4/S9 N-terminal domain The crystal structure of ribosomal protein S4 reveals a family 2, PF00281: Ribosomal protein L5 index pos1 pos2 score npdbs avgdist mindist nshort 0 132 19 9.654120 0 - - 0 #487 PF00163 PF03719 238 1 9.652861 family 1, PF00163: Ribosomal protein S4/S9 N-terminal domain The crystal structure of ribosomal protein S4 reveals a family 2, PF03719: Ribosomal protein S5, C-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 132 103 9.652862 1 30.7015 30.7015 0 #488 PF00347 PF00687 228 1 9.646338 family 1, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene family 2, PF00687: Ribosomal protein L1p/L10e family index pos1 pos2 score npdbs avgdist mindist nshort 0 172 547 9.646338 0 - - 0 489 PF00572 PF06418 231 1 9.646293 family 1, PF00572: Ribosomal protein L13 family 2, PF06418: CTP synthase N-terminus Thr-431 and Arg-433 are part of a conserved sequence motif index pos1 pos2 score npdbs avgdist mindist nshort 0 204 395 9.646293 0 - - 0 #490 PF02446 PF02606 55 1 9.645870 family 1, PF02446: 4-alpha-glucanotransferase Disproportionating enzyme (4-alpha-glucanotransferase; EC family 2, PF02606: Tetraacyldisaccharide-1-P 4'-kinase Accumulation of a lipid A precursor lacking the index pos1 pos2 score npdbs avgdist mindist nshort 0 529 250 9.645871 0 - - 0 491 PF01450 PF08212 46 1 9.637929 family 1, PF01450: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid family 2, PF08212: Lipocalin-like domain index pos1 pos2 score npdbs avgdist mindist nshort 0 18 60 9.637930 0 - - 0 492 PF02390 PF04362 47 1 9.630676 family 1, PF02390: Putative methyltransferase family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 126 20 9.630677 0 - - 0 493 PF00218 PF06509 50 1 9.630540 family 1, PF00218: Indole-3-glycerol phosphate synthase family 2, PF06509: HtpX N-terminus Isolation, characterization, and sequence of an Escherichia index pos1 pos2 score npdbs avgdist mindist nshort 0 17 72 9.630540 0 - - 0 494 PF03023 PF03702 70 1 9.629302 family 1, PF03023: MviN-like protein A Salmonella typhimurium virulence gene linked to flg. family 2, PF03702: Uncharacterised protein family (UPF0075) index pos1 pos2 score npdbs avgdist mindist nshort 0 446 698 9.629303 0 - - 0 #495 PF01790 PF02965 91 1 9.627698 family 1, PF01790: Prolipoprotein diacylglyceryl transferase family 2, PF02965: Vitamin B12 dependent methionine synthase, activation domain The structure of the C-terminal domain of methionine index pos1 pos2 score npdbs avgdist mindist nshort 0 565 27 9.627698 0 - - 0 496 PF01245 PF01964 114 1 9.625891 family 1, PF01245: Ribosomal protein L19 family 2, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes index pos1 pos2 score npdbs avgdist mindist nshort 0 76 306 9.625892 0 - - 0 497 PF01264 PF08298 49 1 9.622529 family 1, PF01264: Chorismate synthase family 2, PF08298: PrkA AAA domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 467 264 9.622530 0 - - 0 #498 PF00238 PF00281 285 1 9.609917 family 1, PF00238: Ribosomal protein L14p/L23e family 2, PF00281: Ribosomal protein L5 index pos1 pos2 score npdbs avgdist mindist nshort 0 253 7 9.609918 1 135.2780 135.2780 0 499 PF02367 PF05195 63 1 9.606272 family 1, PF02367: Uncharacterised P-loop hydrolase UPF0079 family 2, PF05195: Aminopeptidase P, N-terminal domain Structure and mechanism of a proline-specific index pos1 pos2 score npdbs avgdist mindist nshort 0 234 129 9.606273 0 - - 0 500 PF01964 PF02091 84 1 9.601016 family 1, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes family 2, PF02091: Glycyl-tRNA synthetase alpha subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 306 271 9.601016 0 - - 0 #501 PF01553 PF02650 64 1 9.577106 family 1, PF01553: Acyltransferase Barth syndrome may be due to an acyltransferase deficiency. family 2, PF02650: Uncharacterized BCR, COG1481 index pos1 pos2 score npdbs avgdist mindist nshort 0 103 25 9.577107 0 - - 0 502 PF01619 PF01964 85 1 9.574951 family 1, PF01619: Proline dehydrogenase Sequence analysis identifies the proline dehydrogenase and family 2, PF01964: ThiC family Structural genes for thiamine biosynthetic enzymes index pos1 pos2 score npdbs avgdist mindist nshort 0 577 306 9.574952 0 - - 0 503 PF00587 PF04401 47 1 9.574841 family 1, PF00587: tRNA synthetase class II core domain (G, H, P, S and T) Eleven down and nine to go. family 2, PF04401: Protein of unknown function (DUF540) index pos1 pos2 score npdbs avgdist mindist nshort 0 712 114 9.574842 0 - - 0 504 PF01450 PF02503 101 1 9.561717 family 1, PF01450: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid family 2, PF02503: Polyphosphate kinase Transcription of ppk from Acinetobacter sp. strain ADP1, index pos1 pos2 score npdbs avgdist mindist nshort 0 314 408 9.561718 0 - - 0 505 PF01142 PF02568 50 1 9.551356 family 1, PF01142: tRNA pseudouridine synthase D (TruD) A novel unanticipated type of pseudouridine synthase with family 2, PF02568: Thiamine biosynthesis protein (ThiI) Characterization of thiI, a new gene involved in thiazole index pos1 pos2 score npdbs avgdist mindist nshort 0 295 122 9.551356 0 - - 0 506 PF02503 PF03969 61 1 9.549647 family 1, PF02503: Polyphosphate kinase Transcription of ppk from Acinetobacter sp. strain ADP1, family 2, PF03969: AFG1-like ATPase AFG1, a new member of the SEC18-NSF, PAS1, CDC48-VCP, TBP index pos1 pos2 score npdbs avgdist mindist nshort 0 110 1120 9.549648 0 - - 0 507 PF02401 PF04039 63 1 9.544057 family 1, PF02401: LytB protein Identification of the Escherichia coli lytB gene, which is family 2, PF04039: Domain related to MnhB subunit of Na+/H+ antiporter A putative multisubunit Na+/H+ antiporter from index pos1 pos2 score npdbs avgdist mindist nshort 0 346 12 9.544058 0 - - 0 508 PF00710 PF02568 78 1 9.524201 family 1, PF00710: Asparaginase family 2, PF02568: Thiamine biosynthesis protein (ThiI) Characterization of thiI, a new gene involved in thiazole index pos1 pos2 score npdbs avgdist mindist nshort 0 118 218 9.524202 0 - - 0 509 PF02091 PF02590 102 1 9.520346 family 1, PF02091: Glycyl-tRNA synthetase alpha subunit family 2, PF02590: Uncharacterized ACR, COG1576 index pos1 pos2 score npdbs avgdist mindist nshort 0 45 178 9.520348 0 - - 0 #510 PF01326 PF06798 46 1 9.511674 family 1, PF01326: Pyruvate phosphate dikinase, PEP/pyruvate binding domain Swiveling-domain mechanism for enzymatic phosphotransfer family 2, PF06798: PrkA serine protein kinase C-terminal domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 540 26 9.511675 0 - - 0 *511 PF06798 PF08298 51 1 9.510193 family 1, PF06798: PrkA serine protein kinase C-terminal domain Cloning and characterization of the Bacillus subtilis prkA family 2, PF08298: PrkA AAA domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 195 355 9.510194 0 - - 0 512 PF00731 PF04293 52 1 9.502173 family 1, PF00731: AIR carboxylase Crystal structure of Escherichia coli PurE, an unusual family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 23 296 9.502174 0 - - 0 513 PF01784 PF01790 137 1 9.501296 family 1, PF01784: NIF3 (NGG1p interacting factor 3) Transcriptional activation by yeast PDR1p is inhibited by family 2, PF01790: Prolipoprotein diacylglyceryl transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 152 565 9.501298 0 - - 0 514 PF01523 PF01784 73 1 9.491855 family 1, PF01523: Putative modulator of DNA gyrase Evidence for involvement of Escherichia coli genes pmbA, family 2, PF01784: NIF3 (NGG1p interacting factor 3) Transcriptional activation by yeast PDR1p is inhibited by index pos1 pos2 score npdbs avgdist mindist nshort 0 391 715 9.491856 0 - - 0 515 PF03548 PF03658 51 1 9.491065 family 1, PF03548: Outer membrane lipoprotein carrier protein LolA family 2, PF03658: Uncharacterised protein family (UPF0125) index pos1 pos2 score npdbs avgdist mindist nshort 0 153 79 9.491065 0 - - 0 516 PF01162 PF01316 59 1 9.489856 family 1, PF01162: PET112 family, C terminal region family 2, PF01316: Arginine repressor, DNA binding domain Solution structure of the DNA-binding domain and model for index pos1 pos2 score npdbs avgdist mindist nshort 0 60 46 9.489857 0 - - 0 517 PF00285 PF01916 59 1 9.485255 family 1, PF00285: Citrate synthase family 2, PF01916: Deoxyhypusine synthase Crystal structure of the NAD complex of human deoxyhypusine index pos1 pos2 score npdbs avgdist mindist nshort 0 432 589 9.485256 0 - - 0 518 PF01175 PF01790 66 1 9.483411 family 1, PF01175: Urocanase family 2, PF01790: Prolipoprotein diacylglyceryl transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 431 372 9.483412 0 - - 0 519 PF02390 PF05673 47 1 9.471040 family 1, PF02390: Putative methyltransferase family 2, PF05673: Protein of unknown function (DUF815) index pos1 pos2 score npdbs avgdist mindist nshort 0 598 57 9.471041 0 - - 0 520 PF02565 PF03702 68 1 9.468542 family 1, PF02565: Recombination protein O Molecular analysis of the Escherichia coli recO gene. family 2, PF03702: Uncharacterised protein family (UPF0075) index pos1 pos2 score npdbs avgdist mindist nshort 0 272 443 9.468542 0 - - 0 521 PF00768 PF04362 50 1 9.466503 family 1, PF00768: D-alanyl-D-alanine carboxypeptidase family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 551 45 9.466504 0 - - 0 522 PF02646 PF06434 48 1 9.465515 family 1, PF02646: RmuC family Genes involved in the determination of the rate of family 2, PF06434: Aconitate hydratase 2 N-terminus Biochemical and spectroscopic characterization of index pos1 pos2 score npdbs avgdist mindist nshort 0 355 189 9.465515 0 - - 0 523 PF01725 PF02556 64 1 9.465060 family 1, PF01725: Ham1 family HAM1, the gene controlling 6-N-hydroxylaminopurine family 2, PF02556: Preprotein translocase subunit SecB Characterization of the Escherichia coli protein-export index pos1 pos2 score npdbs avgdist mindist nshort 0 472 224 9.465060 0 - - 0 524 PF01985 PF08267 67 1 9.454059 family 1, PF01985: CRS1 / YhbY domain Crystal structure of E. coli YhbY: a representative of a family 2, PF08267: Cobalamin-independent synthase, N-terminal domain Crystal structures of cobalamin-independent methionine index pos1 pos2 score npdbs avgdist mindist nshort 0 61 411 9.454060 0 - - 0 525 PF01599 PF01916 52 1 9.451779 family 1, PF01599: Ribosomal protein S27a Characterization and expression of two chicken cDNAs family 2, PF01916: Deoxyhypusine synthase Crystal structure of the NAD complex of human deoxyhypusine index pos1 pos2 score npdbs avgdist mindist nshort 0 39 151 9.451780 0 - - 0 526 PF01916 PF07650 66 1 9.451679 family 1, PF01916: Deoxyhypusine synthase Crystal structure of the NAD complex of human deoxyhypusine family 2, PF07650: KH domain Conserved structures and diversity of functions of index pos1 pos2 score npdbs avgdist mindist nshort 0 589 28 9.451680 0 - - 0 *527 PF00680 PF08440 50 1 9.449842 family 1, PF00680: RNA dependent RNA polymerase family 2, PF08440: Potyviridae polyprotein index pos1 pos2 score npdbs avgdist mindist nshort 0 835 11 9.449843 0 - - 0 528 PF01592 PF04293 48 1 9.449235 family 1, PF01592: NifU-like N terminal domain A modular domain of NifU, a nitrogen fixation cluster family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 91 496 9.449235 0 - - 0 529 PF03193 PF04608 57 1 9.438080 family 1, PF03193: Protein of unknown function, DUF258 family 2, PF04608: Phosphatidylglycerophosphatase A The pgpA and pgpB genes of Escherichia coli are not index pos1 pos2 score npdbs avgdist mindist nshort 0 268 7 9.438081 0 - - 0 530 PF02600 PF05697 86 1 9.438041 family 1, PF02600: Disulfide bond formation protein DsbB Two cysteines in each periplasmic domain of the membrane family 2, PF05697: Bacterial trigger factor protein (TF) Trigger Factor and DnaK possess overlapping substrate pools index pos1 pos2 score npdbs avgdist mindist nshort 0 318 13 9.438042 0 - - 0 #531 PF05191 PF08298 49 1 9.434102 family 1, PF05191: Adenylate kinase, active site lid Crystal structures of Bacillus stearothermophilus adenylate family 2, PF08298: PrkA AAA domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 47 9 9.434103 0 - - 0 #532 PF00163 PF00333 239 1 9.424025 family 1, PF00163: Ribosomal protein S4/S9 N-terminal domain The crystal structure of ribosomal protein S4 reveals a family 2, PF00333: Ribosomal protein S5, N-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 60 56 9.424025 1 32.9761 32.9761 0 533 PF00318 PF01316 83 1 9.422266 family 1, PF00318: Ribosomal protein S2 family 2, PF01316: Arginine repressor, DNA binding domain Solution structure of the DNA-binding domain and model for index pos1 pos2 score npdbs avgdist mindist nshort 0 321 46 9.422267 0 - - 0 534 PF03953 PF04379 70 1 9.421879 family 1, PF03953: Tubulin/FtsZ family, C-terminal domain Structure of the alphabeta tubulin dimer by electron family 2, PF04379: Protein of unknown function (DUF525) A family of mammalian F-box proteins. index pos1 pos2 score npdbs avgdist mindist nshort 0 180 46 9.421880 0 - - 0 535 PF03364 PF04362 47 1 9.405927 family 1, PF03364: Streptomyces cyclase/dehydrase family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 28 20 9.405928 0 - - 0 536 PF00471 PF03313 112 1 9.402680 family 1, PF00471: Ribosomal protein L33 family 2, PF03313: Serine dehydratase alpha chain index pos1 pos2 score npdbs avgdist mindist nshort 0 53 304 9.402681 0 - - 0 537 PF00764 PF04293 51 1 9.395925 family 1, PF00764: Arginosuccinate synthase A P-loop-like motif in a widespread ATP pyrophosphatase family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 166 19 9.395927 0 - - 0 538 PF02978 PF06418 229 1 9.393174 family 1, PF02978: Signal peptide binding domain Crystal structure of the conserved subdomain of human family 2, PF06418: CTP synthase N-terminus Thr-431 and Arg-433 are part of a conserved sequence motif index pos1 pos2 score npdbs avgdist mindist nshort 0 96 395 9.393175 0 - - 0 #539 PF00163 PF00298 238 1 9.389240 family 1, PF00163: Ribosomal protein S4/S9 N-terminal domain The crystal structure of ribosomal protein S4 reveals a family 2, PF00298: Ribosomal protein L11, RNA binding domain High resolution solution structure of ribosomal protein index pos1 pos2 score npdbs avgdist mindist nshort 0 108 0 9.389240 0 - - 0 540 PF02219 PF04293 45 1 9.388794 family 1, PF02219: Methylenetetrahydrofolate reductase The structure and properties of methylenetetrahydrofolate family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 694 3 9.388796 0 - - 0 541 PF02600 PF02684 66 1 9.376108 family 1, PF02600: Disulfide bond formation protein DsbB Two cysteines in each periplasmic domain of the membrane family 2, PF02684: Lipid-A-disaccharide synthetase Cloning and expression of genes encoding lipid A index pos1 pos2 score npdbs avgdist mindist nshort 0 318 270 9.376108 0 - - 0 542 PF00042 PF02091 51 1 9.373613 family 1, PF00042: Globin Determinants of a protein fold. Unique features of the family 2, PF02091: Glycyl-tRNA synthetase alpha subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 175 34 9.373614 0 - - 0 543 PF03315 PF06835 46 1 9.372613 family 1, PF03315: Serine dehydratase beta chain family 2, PF06835: Protein of unknown function (DUF1239) index pos1 pos2 score npdbs avgdist mindist nshort 0 26 202 9.372614 0 - - 0 544 PF04379 PF04560 71 1 9.367001 family 1, PF04379: Protein of unknown function (DUF525) A family of mammalian F-box proteins. family 2, PF04560: RNA polymerase Rpb2, domain 7 Structural basis of transcription: RNA polymerase II at 2.8 index pos1 pos2 score npdbs avgdist mindist nshort 0 97 143 9.367002 0 - - 0 545 PF01316 PF01790 83 1 9.366985 family 1, PF01316: Arginine repressor, DNA binding domain Solution structure of the DNA-binding domain and model for family 2, PF01790: Prolipoprotein diacylglyceryl transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 46 640 9.366986 0 - - 0 546 PF03548 PF04364 66 1 9.366675 family 1, PF03548: Outer membrane lipoprotein carrier protein LolA family 2, PF04364: DNA polymerase III chi subunit, HolC DnaX complex of Escherichia coli DNA polymerase III index pos1 pos2 score npdbs avgdist mindist nshort 0 153 141 9.366675 0 - - 0 547 PF01170 PF04285 48 1 9.358906 family 1, PF01170: Putative RNA methylase family UPF0020 THUMP - a predicted RNA-binding domain shared by family 2, PF04285: Protein of unknown function (DUF444) index pos1 pos2 score npdbs avgdist mindist nshort 0 769 276 9.358907 0 - - 0 548 PF03350 PF04413 44 1 9.355374 family 1, PF03350: Uncharacterized protein family, UPF0114 family 2, PF04413: 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase) 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 25 314 9.355374 0 - - 0 549 PF01131 PF02650 65 1 9.355353 family 1, PF01131: DNA topoisomerase Three-dimensional structure of the 67K N-terminal fragment family 2, PF02650: Uncharacterized BCR, COG1481 index pos1 pos2 score npdbs avgdist mindist nshort 0 14 387 9.355354 0 - - 0 #550 PF03447 PF08298 47 1 9.350368 family 1, PF03447: Homoserine dehydrogenase, NAD binding domain family 2, PF08298: PrkA AAA domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 259 264 9.350369 0 - - 0 551 PF01264 PF02547 127 1 9.347267 family 1, PF01264: Chorismate synthase family 2, PF02547: Queuosine biosynthesis protein A new function of S-adenosylmethionine: the ribosyl moiety index pos1 pos2 score npdbs avgdist mindist nshort 0 217 521 9.347267 0 - - 0 #552 PF01991 PF01992 66 1 9.343597 family 1, PF01991: ATP synthase (E/31 kDa) subunit The 31-kDa polypeptide is an essential subunit of the family 2, PF01992: ATP synthase (C/AC39) subunit The Saccharomyces cerevisiae VMA6 gene encodes the 36-kDa index pos1 pos2 score npdbs avgdist mindist nshort 0 18 186 9.343597 0 - - 0 553 PF03588 PF04397 44 1 9.343527 family 1, PF03588: Leucyl/phenylalanyl-tRNA protein transferase family 2, PF04397: LytTr DNA-binding domain A novel type of conserved DNA-binding domain in the index pos1 pos2 score npdbs avgdist mindist nshort 0 210 25 9.343528 0 - - 0 554 PF01980 PF03023 47 1 9.342094 family 1, PF01980: Uncharacterised protein family UPF0066 family 2, PF03023: MviN-like protein A Salmonella typhimurium virulence gene linked to flg. index pos1 pos2 score npdbs avgdist mindist nshort 0 95 396 9.342094 0 - - 0 555 PF01411 PF06798 51 1 9.339791 family 1, PF01411: tRNA synthetases class II (A) family 2, PF06798: PrkA serine protein kinase C-terminal domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 368 275 9.339792 0 - - 0 556 PF01975 PF08267 67 1 9.337061 family 1, PF01975: Survival protein SurE A new gene involved in stationary-phase survival located at family 2, PF08267: Cobalamin-independent synthase, N-terminal domain Crystal structures of cobalamin-independent methionine index pos1 pos2 score npdbs avgdist mindist nshort 0 141 377 9.337062 0 - - 0 557 PF01592 PF01704 46 1 9.333530 family 1, PF01592: NifU-like N terminal domain A modular domain of NifU, a nitrogen fixation cluster family 2, PF01704: UTP--glucose-1-phosphate uridylyltransferase Sequence differences between human muscle and liver cDNAs index pos1 pos2 score npdbs avgdist mindist nshort 0 84 498 9.333531 0 - - 0 558 PF00762 PF03883 70 1 9.331250 family 1, PF00762: Ferrochelatase family 2, PF03883: Protein of unknown function (DUF328) index pos1 pos2 score npdbs avgdist mindist nshort 0 96 136 9.331250 0 - - 0 559 PF01316 PF05192 68 1 9.322764 family 1, PF01316: Arginine repressor, DNA binding domain Solution structure of the DNA-binding domain and model for family 2, PF05192: MutS domain III Domain organization and functional analysis of Thermus index pos1 pos2 score npdbs avgdist mindist nshort 0 46 1259 9.322764 0 - - 0 560 PF02401 PF03205 60 1 9.317533 family 1, PF02401: LytB protein Identification of the Escherichia coli lytB gene, which is family 2, PF03205: Molybdopterin guanine dinucleotide synthesis protein B index pos1 pos2 score npdbs avgdist mindist nshort 0 218 40 9.317534 0 - - 0 #561 PF01193 PF01316 84 1 9.315042 family 1, PF01193: RNA polymerase Rpb3/Rpb11 dimerisation domain Structure of the Escherichia coli RNA polymerase alpha family 2, PF01316: Arginine repressor, DNA binding domain Solution structure of the DNA-binding domain and model for index pos1 pos2 score npdbs avgdist mindist nshort 0 481 47 9.315043 0 - - 0 562 PF02742 PF04002 52 1 9.310216 family 1, PF02742: Iron dependent repressor, metal binding and dimerisation domain Structures of the apo- and the metal ion-activated forms of family 2, PF04002: RadC, DNA repair protein Tandem repeat recombination induced by replication fork index pos1 pos2 score npdbs avgdist mindist nshort 0 38 64 9.310217 0 - - 0 #563 PF02283 PF02607 73 1 9.306096 family 1, PF02283: Cobinamide kinase / cobinamide phosphate guanyltransferase Three-dimensional structure of adenosylcobinamide family 2, PF02607: B12 binding domain How a protein binds B12: A 3.0 A X-ray structure of index pos1 pos2 score npdbs avgdist mindist nshort 0 66 71 9.306097 0 - - 0 564 PF00670 PF04079 82 1 9.304579 family 1, PF00670: S-adenosyl-L-homocysteine hydrolase, NAD binding domain family 2, PF04079: Putative transcriptional regulators (Ypuh-like) index pos1 pos2 score npdbs avgdist mindist nshort 0 66 196 9.304580 0 - - 0 565 PF01293 PF02575 64 1 9.304348 family 1, PF01293: Phosphoenolpyruvate carboxykinase Snapshot of an enzyme reaction intermediate in the family 2, PF02575: Uncharacterised BCR, YbaB family COG0718 index pos1 pos2 score npdbs avgdist mindist nshort 0 179 111 9.304349 0 - - 0 566 PF03969 PF05494 53 1 9.287626 family 1, PF03969: AFG1-like ATPase AFG1, a new member of the SEC18-NSF, PAS1, CDC48-VCP, TBP family 2, PF05494: Toluene tolerance, Ttg2 Mechanisms for solvent tolerance in bacteria. index pos1 pos2 score npdbs avgdist mindist nshort 0 1325 188 9.287627 0 - - 0 567 PF02620 PF03776 59 1 9.284486 family 1, PF02620: Uncharacterized ACR, COG1399 family 2, PF03776: Septum formation topological specificity factor MinE A division inhibitor and a topological specificity factor index pos1 pos2 score npdbs avgdist mindist nshort 0 292 71 9.284487 0 - - 0 568 PF00670 PF01628 64 1 9.280714 family 1, PF00670: S-adenosyl-L-homocysteine hydrolase, NAD binding domain family 2, PF01628: HrcA protein C terminal domain hrcA, the first gene of the Bacillus subtilis dnaK operon index pos1 pos2 score npdbs avgdist mindist nshort 0 66 193 9.280715 0 - - 0 569 PF02091 PF02153 96 1 9.278691 family 1, PF02091: Glycyl-tRNA synthetase alpha subunit family 2, PF02153: Prephenate dehydrogenase index pos1 pos2 score npdbs avgdist mindist nshort 0 45 10 9.278692 0 - - 0 570 PF01000 PF04293 52 1 9.277359 family 1, PF01000: RNA polymerase Rpb3/RpoA insert domain Structure of the Escherichia coli RNA polymerase alpha family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 101 539 9.277359 0 - - 0 571 PF01784 PF02600 66 1 9.270982 family 1, PF01784: NIF3 (NGG1p interacting factor 3) Transcriptional activation by yeast PDR1p is inhibited by family 2, PF02600: Disulfide bond formation protein DsbB Two cysteines in each periplasmic domain of the membrane index pos1 pos2 score npdbs avgdist mindist nshort 0 17 249 9.270983 0 - - 0 572 PF01175 PF06418 77 1 9.267638 family 1, PF01175: Urocanase family 2, PF06418: CTP synthase N-terminus Thr-431 and Arg-433 are part of a conserved sequence motif index pos1 pos2 score npdbs avgdist mindist nshort 0 820 23 9.267639 0 - - 0 573 PF01208 PF04293 47 1 9.259781 family 1, PF01208: Uroporphyrinogen decarboxylase (URO-D) family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 705 556 9.259782 0 - - 0 574 PF04285 PF06071 49 1 9.258153 family 1, PF04285: Protein of unknown function (DUF444) family 2, PF06071: Protein of unknown function (DUF933) index pos1 pos2 score npdbs avgdist mindist nshort 0 446 72 9.258154 0 - - 0 #575 PF04565 PF05000 290 1 9.247753 family 1, PF04565: RNA polymerase Rpb2, domain 3 Structural basis of transcription: RNA polymerase II at 2.8 family 2, PF05000: RNA polymerase Rpb1, domain 4 Structural modules of the large subunits of RNA polymerase. index pos1 pos2 score npdbs avgdist mindist nshort 0 16 19 9.247754 2 45.8311 40.6071 0 #576 PF00398 PF03588 84 1 9.245299 family 1, PF00398: Ribosomal RNA adenine dimethylase Solution structure of an rRNA methyltransferase (ErmAM) family 2, PF03588: Leucyl/phenylalanyl-tRNA protein transferase index pos1 pos2 score npdbs avgdist mindist nshort 0 664 16 9.245300 0 - - 0 577 PF02600 PF06968 73 1 9.243280 family 1, PF02600: Disulfide bond formation protein DsbB Two cysteines in each periplasmic domain of the membrane family 2, PF06968: Biotin and Thiamin Synthesis associated domain The PLP-dependent biotin synthase from Escherichia coli: index pos1 pos2 score npdbs avgdist mindist nshort 0 318 50 9.243281 0 - - 0 578 PF00988 PF04293 51 1 9.225009 family 1, PF00988: Carbamoyl-phosphate synthase small chain, CPSase domain Mammalian carbamyl phosphate synthetase (CPS). DNA sequence family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 247 282 9.225010 0 - - 0 579 PF02091 PF04362 52 1 9.218759 family 1, PF02091: Glycyl-tRNA synthetase alpha subunit family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 45 20 9.218760 0 - - 0 #580 PF01432 PF03702 73 1 9.217163 family 1, PF01432: Peptidase family M3 Evolutionary families of metallopeptidases. family 2, PF03702: Uncharacterised protein family (UPF0075) index pos1 pos2 score npdbs avgdist mindist nshort 0 755 698 9.217164 0 - - 0 581 PF01238 PF01641 66 1 9.214054 family 1, PF01238: Phosphomannose isomerase type I The x-ray crystal structure of phosphomannose isomerase family 2, PF01641: SelR domain Novel selenoproteins identified in silico and in vivo by index pos1 pos2 score npdbs avgdist mindist nshort 0 297 64 9.214055 0 - - 0 582 PF01450 PF04359 50 1 9.211417 family 1, PF01450: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid family 2, PF04359: Protein of unknown function (DUF493) index pos1 pos2 score npdbs avgdist mindist nshort 0 314 18 9.211417 0 - - 0 #583 PF02130 PF02446 89 1 9.210417 family 1, PF02130: Uncharacterized protein family UPF0054 family 2, PF02446: 4-alpha-glucanotransferase Disproportionating enzyme (4-alpha-glucanotransferase; EC index pos1 pos2 score npdbs avgdist mindist nshort 0 176 529 9.210418 0 - - 0 584 PF00669 PF02628 52 1 9.206902 family 1, PF00669: Bacterial flagellin N-terminus Spinning tails. family 2, PF02628: Cytochrome oxidase assembly protein Isolation and sequence of ctaA, a gene required for index pos1 pos2 score npdbs avgdist mindist nshort 0 53 561 9.206904 0 - - 0 585 PF02390 PF08298 48 1 9.205495 family 1, PF02390: Putative methyltransferase family 2, PF08298: PrkA AAA domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 126 338 9.205496 0 - - 0 586 PF00573 PF06798 51 1 9.202574 family 1, PF00573: Ribosomal protein L4/L1 family Yeast ribosomal proteins L4, L17, L20, and L25 exhibit family 2, PF06798: PrkA serine protein kinase C-terminal domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 52 26 9.202575 0 - - 0 587 PF00464 PF00816 46 1 9.199711 family 1, PF00464: Serine hydroxymethyltransferase family 2, PF00816: H-NS histone family Solution structure of the DNA binding domain of a index pos1 pos2 score npdbs avgdist mindist nshort 0 927 157 9.199711 0 - - 0 588 PF00742 PF04279 54 1 9.194242 family 1, PF00742: Homoserine dehydrogenase family 2, PF04279: Intracellular septation protein A Identification and characterization of ispA, a Shigella index pos1 pos2 score npdbs avgdist mindist nshort 0 66 116 9.194243 0 - - 0 589 PF00953 PF06798 50 1 9.189665 family 1, PF00953: Glycosyl transferase family 4 A family of UDP-GlcNAc/MurNAc: polyisoprenol-P family 2, PF06798: PrkA serine protein kinase C-terminal domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 69 273 9.189666 0 - - 0 590 PF03588 PF03840 74 1 9.185628 family 1, PF03588: Leucyl/phenylalanyl-tRNA protein transferase family 2, PF03840: Preprotein translocase SecG subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 16 46 9.185629 0 - - 0 #591 PF00203 PF03947 350 1 9.180525 family 1, PF00203: Ribosomal protein S19 family 2, PF03947: Ribosomal Proteins L2, C-terminal domain index pos1 pos2 score npdbs avgdist mindist nshort 0 94 258 9.180526 0 - - 0 #592 PF00075 PF00816 46 1 9.179564 family 1, PF00075: RNase H family 2, PF00816: H-NS histone family Solution structure of the DNA binding domain of a index pos1 pos2 score npdbs avgdist mindist nshort 0 38 157 9.179565 0 - - 0 593 PF03279 PF06026 68 1 9.179534 family 1, PF03279: Bacterial lipid A biosynthesis acyltransferase family 2, PF06026: Ribose 5-phosphate isomerase A (phosphoriboisomerase A) Crystal structure of D-ribose-5-phosphate isomerase (RpiA) index pos1 pos2 score npdbs avgdist mindist nshort 0 165 129 9.179534 0 - - 0 *594 PF02786 PF02787 254 1 9.172117 family 1, PF02786: Carbamoyl-phosphate synthase L chain, ATP binding domain Three-dimensional structure of the biotin carboxylase family 2, PF02787: Carbamoyl-phosphate synthetase large chain, oligomerisation domain The structure of carbamoyl phosphate synthetase determined index pos1 pos2 score npdbs avgdist mindist nshort 0 591 183 9.172118 0 - - 0 #595 PF01000 PF01316 83 1 9.168012 family 1, PF01000: RNA polymerase Rpb3/RpoA insert domain Structure of the Escherichia coli RNA polymerase alpha family 2, PF01316: Arginine repressor, DNA binding domain Solution structure of the DNA-binding domain and model for index pos1 pos2 score npdbs avgdist mindist nshort 0 216 46 9.168013 0 - - 0 596 PF00977 PF01293 72 1 9.166340 family 1, PF00977: Histidine biosynthesis protein Paralogous histidine biosynthetic genes: evolutionary family 2, PF01293: Phosphoenolpyruvate carboxykinase Snapshot of an enzyme reaction intermediate in the index pos1 pos2 score npdbs avgdist mindist nshort 0 156 176 9.166340 0 - - 0 597 PF00162 PF01316 86 1 9.162601 family 1, PF00162: Phosphoglycerate kinase family 2, PF01316: Arginine repressor, DNA binding domain Solution structure of the DNA-binding domain and model for index pos1 pos2 score npdbs avgdist mindist nshort 0 596 63 9.162602 0 - - 0 598 PF04608 PF06144 71 1 9.159829 family 1, PF04608: Phosphatidylglycerophosphatase A The pgpA and pgpB genes of Escherichia coli are not family 2, PF06144: DNA polymerase III, delta subunit The delta and delta ' subunits of the DNA polymerase III index pos1 pos2 score npdbs avgdist mindist nshort 0 7 409 9.159829 0 - - 0 599 PF01134 PF01316 72 1 9.155629 family 1, PF01134: Glucose inhibited division protein A family 2, PF01316: Arginine repressor, DNA binding domain Solution structure of the DNA-binding domain and model for index pos1 pos2 score npdbs avgdist mindist nshort 0 622 63 9.155629 0 - - 0 600 PF01432 PF04608 61 1 9.154293 family 1, PF01432: Peptidase family M3 Evolutionary families of metallopeptidases. family 2, PF04608: Phosphatidylglycerophosphatase A The pgpA and pgpB genes of Escherichia coli are not index pos1 pos2 score npdbs avgdist mindist nshort 0 143 7 9.154294 0 - - 0 601 PF00814 PF04293 52 1 9.150162 family 1, PF00814: Glycoprotease family Gleaning non-trivial structural, functional and family 2, PF04293: SpoVR like protein Cloning and characterization of spoVR, a gene from Bacillus index pos1 pos2 score npdbs avgdist mindist nshort 0 842 470 9.150162 0 - - 0 602 PF02554 PF02572 51 1 9.149770 family 1, PF02554: Carbon starvation protein CstA Molecular and functional characterization of a carbon family 2, PF02572: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP Cobalamin (vitamin B12) biosynthesis: identification and index pos1 pos2 score npdbs avgdist mindist nshort 0 649 342 9.149771 0 - - 0 603 PF01761 PF04608 68 1 9.144238 family 1, PF01761: 3-dehydroquinate synthase Cloning and characterisation of the Neisseria gonorrhoeae family 2, PF04608: Phosphatidylglycerophosphatase A The pgpA and pgpB genes of Escherichia coli are not index pos1 pos2 score npdbs avgdist mindist nshort 0 514 7 9.144238 0 - - 0 604 PF01409 PF08298 51 1 9.137701 family 1, PF01409: tRNA synthetases class II core domain (F) family 2, PF08298: PrkA AAA domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 89 264 9.137702 0 - - 0 605 PF01305 PF02433 45 1 9.118180 family 1, PF01305: Ribosomal protein L15 amino terminal region family 2, PF02433: Cytochrome C oxidase, mono-heme subunit/FixO A cytochrome cbb3 (cytochrome c) terminal oxidase in index pos1 pos2 score npdbs avgdist mindist nshort 0 70 208 9.118181 0 - - 0 #606 PF01715 PF03710 80 1 9.118144 family 1, PF01715: IPP transferase The modified nucleoside family 2, PF03710: Glutamate-ammonia ligase adenylyltransferase index pos1 pos2 score npdbs avgdist mindist nshort 0 744 361 9.118144 0 - - 0 607 PF01398 PF01743 45 1 9.117146 family 1, PF01398: Mov34/MPN/PAD-1 family Homologues of 26S proteasome subunits are regulators of family 2, PF01743: Poly A polymerase family Identification of the gene for an Escherichia coli poly(A) index pos1 pos2 score npdbs avgdist mindist nshort 0 311 121 9.117146 0 - - 0 #608 PF00464 PF05726 93 1 9.112559 family 1, PF00464: Serine hydroxymethyltransferase family 2, PF05726: Pirin C-terminal cupin domain index pos1 pos2 score npdbs avgdist mindist nshort 0 477 227 9.112561 0 - - 0 #609 PF00329 PF01257 117 1 9.112025 family 1, PF00329: Respiratory-chain NADH dehydrogenase, 30 Kd subunit family 2, PF01257: Respiratory-chain NADH dehydrogenase 24 Kd subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 116 207 9.112026 0 - - 0 610 PF02092 PF08267 67 1 9.109553 family 1, PF02092: Glycyl-tRNA synthetase beta subunit family 2, PF08267: Cobalamin-independent synthase, N-terminal domain Crystal structures of cobalamin-independent methionine index pos1 pos2 score npdbs avgdist mindist nshort 0 520 411 9.109554 0 - - 0 611 PF00471 PF00490 149 1 9.108776 family 1, PF00471: Ribosomal protein L33 family 2, PF00490: Delta-aminolevulinic acid dehydratase index pos1 pos2 score npdbs avgdist mindist nshort 0 53 371 9.108777 0 - - 0 612 PF00762 PF01250 152 1 9.103684 family 1, PF00762: Ferrochelatase family 2, PF01250: Ribosomal protein S6 Crystal structure of the ribosomal protein S6 from Thermus index pos1 pos2 score npdbs avgdist mindist nshort 0 96 93 9.103684 0 - - 0 613 PF01409 PF04362 52 1 9.099243 family 1, PF01409: tRNA synthetases class II core domain (F) family 2, PF04362: Bacterial Fe(2+) trafficking Small genes/gene-products in Escherichia coli K-12. index pos1 pos2 score npdbs avgdist mindist nshort 0 89 20 9.099244 0 - - 0 614 PF00953 PF03668 112 1 9.098276 family 1, PF00953: Glycosyl transferase family 4 A family of UDP-GlcNAc/MurNAc: polyisoprenol-P family 2, PF03668: P-loop ATPase protein family index pos1 pos2 score npdbs avgdist mindist nshort 0 23 275 9.098277 0 - - 0 #615 PF00749 PF00935 58 1 9.097380 family 1, PF00749: tRNA synthetases class I (E and Q), catalytic domain How glutaminyl-tRNA synthetase selects glutamine. family 2, PF00935: Ribosomal protein L44 index pos1 pos2 score npdbs avgdist mindist nshort 0 26 32 9.097381 0 - - 0 616 PF04093 PF06026 66 1 9.095666 family 1, PF04093: rod shape-determining protein MreD family 2, PF06026: Ribose 5-phosphate isomerase A (phosphoriboisomerase A) Crystal structure of D-ribose-5-phosphate isomerase (RpiA) index pos1 pos2 score npdbs avgdist mindist nshort 0 56 79 9.095667 0 - - 0 617 PF01175 PF03477 77 1 9.095002 family 1, PF01175: Urocanase family 2, PF03477: ATP cone domain The ATP-cone: an evolutionarily mobile, ATP-binding index pos1 pos2 score npdbs avgdist mindist nshort 0 820 150 9.095002 0 - - 0 618 PF01264 PF03755 83 1 9.091672 family 1, PF01264: Chorismate synthase family 2, PF03755: YicC-like family, N-terminal region Three genes preceding pyrE on the Escherichia coli index pos1 pos2 score npdbs avgdist mindist nshort 0 181 72 9.091673 0 - - 0 619 PF00762 PF02965 91 1 9.090497 family 1, PF00762: Ferrochelatase family 2, PF02965: Vitamin B12 dependent methionine synthase, activation domain The structure of the C-terminal domain of methionine index pos1 pos2 score npdbs avgdist mindist nshort 0 96 105 9.090498 0 - - 0 #620 PF02636 PF03279 46 1 9.088597 family 1, PF02636: Uncharacterized ACR, COG1565 family 2, PF03279: Bacterial lipid A biosynthesis acyltransferase index pos1 pos2 score npdbs avgdist mindist nshort 0 51 165 9.088597 0 - - 0 621 PF00762 PF02777 181 1 9.084806 family 1, PF00762: Ferrochelatase family 2, PF02777: Iron/manganese superoxide dismutases, C-terminal domain Refined crystal structure of a superoxide dismutase from index pos1 pos2 score npdbs avgdist mindist nshort 0 127 61 9.084807 0 - - 0 622 PF04608 PF05192 67 1 9.084695 family 1, PF04608: Phosphatidylglycerophosphatase A The pgpA and pgpB genes of Escherichia coli are not family 2, PF05192: MutS domain III Domain organization and functional analysis of Thermus index pos1 pos2 score npdbs avgdist mindist nshort 0 7 129 9.084696 0 - - 0 #623 PF00203 PF00318 326 1 9.082347 family 1, PF00203: Ribosomal protein S19 family 2, PF00318: Ribosomal protein S2 index pos1 pos2 score npdbs avgdist mindist nshort 0 77 192 9.082348 1 89.6860 89.6860 0 624 PF00816 PF01512 46 1 9.082128 family 1, PF00816: H-NS histone family Solution structure of the DNA binding domain of a family 2, PF01512: Respiratory-chain NADH dehydrogenase 51 Kd subunit index pos1 pos2 score npdbs avgdist mindist nshort 0 157 374 9.082129 0 - - 0 #625 PF00189 PF00338 268 1 9.077004 family 1, PF00189: Ribosomal protein S3, C-terminal domain Conserved structures and diversity of functions of family 2, PF00338: Ribosomal protein S10p/S20e index pos1 pos2 score npdbs avgdist mindist nshort 0 101 6 9.077004 1 32.1588 32.1588 0 626 PF00768 PF06798 47 1 9.073753 family 1, PF00768: D-alanyl-D-alanine carboxypeptidase family 2, PF06798: PrkA serine protein kinase C-terminal domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 551 222 9.073754 0 - - 0 627 PF01450 PF03562 57 1 9.071479 family 1, PF01450: Acetohydroxy acid isomeroreductase, catalytic domain The crystal structure of plant acetohydroxy acid family 2, PF03562: MltA N-terminal domain Demonstration of molecular interactions between the murein index pos1 pos2 score npdbs avgdist mindist nshort 0 314 189 9.071479 0 - - 0 628 PF01791 PF02606 53 1 9.070453 family 1, PF01791: DeoC/LacD family aldolase Deoxyribose 5-phosphate aldolase of Bacillus cereus: family 2, PF02606: Tetraacyldisaccharide-1-P 4'-kinase Accumulation of a lipid A precursor lacking the index pos1 pos2 score npdbs avgdist mindist nshort 0 274 265 9.070454 0 - - 0 #629 PF00221 PF01175 81 1 9.069041 family 1, PF00221: Phenylalanine and histidine ammonia-lyase family 2, PF01175: Urocanase index pos1 pos2 score npdbs avgdist mindist nshort 0 1005 820 9.069042 0 - - 0 630 PF00342 PF02955 69 1 9.065292 family 1, PF00342: Phosphoglucose isomerase Crystallographic structure analysis of glucose 6-phosphate family 2, PF02955: Prokaryotic glutathione synthetase, ATP-grasp domain Three-dimensional structure of the glutathione synthetase index pos1 pos2 score npdbs avgdist mindist nshort 0 742 38 9.065293 0 - - 0 #631 PF00164 PF03749 70 1 9.064598 family 1, PF00164: Ribosomal protein S12 family 2, PF03749: Sugar fermentation stimulation protein Nucleotide sequence and characterization of the sfs1 gene: index pos1 pos2 score npdbs avgdist mindist nshort 0 110 4 9.064599 0 - - 0 #632 PF00177 PF00416 298 1 9.058895 family 1, PF00177: Ribosomal protein S7p/S5e The structure of ribosomal protein S7 at 1.9 A resolution family 2, PF00416: Ribosomal protein S13/S18 index pos1 pos2 score npdbs avgdist mindist nshort 0 344 215 9.058896 1 38.8444 38.8444 0 633 PF01208 PF02556 72 1 9.058178 family 1, PF01208: Uroporphyrinogen decarboxylase (URO-D) family 2, PF02556: Preprotein translocase subunit SecB Characterization of the Escherichia coli protein-export index pos1 pos2 score npdbs avgdist mindist nshort 0 483 191 9.058179 0 - - 0 *634 PF00440 PF02909 52 1 9.057755 family 1, PF00440: Bacterial regulatory proteins, tetR family family 2, PF02909: Tetracyclin repressor, C-terminal all-alpha domain Structure of the Tet repressor-tetracycline complex and index pos1 pos2 score npdbs avgdist mindist nshort 0 44 34 9.057756 0 - - 0 635 PF01175 PF02075 53 1 9.052113 family 1, PF01175: Urocanase family 2, PF02075: Crossover junction endodeoxyribonuclease RuvC index pos1 pos2 score npdbs avgdist mindist nshort 0 876 175 9.052113 0 - - 0 636 PF00309 PF03702 57 1 9.041005 family 1, PF00309: Sigma-54 factor, Activator interacting domain (AID) Binding of transcriptional activators to sigma 54 in the family 2, PF03702: Uncharacterised protein family (UPF0075) index pos1 pos2 score npdbs avgdist mindist nshort 0 33 698 9.041006 0 - - 0 #637 PF02091 PF03710 62 1 9.033381 family 1, PF02091: Glycyl-tRNA synthetase alpha subunit family 2, PF03710: Glutamate-ammonia ligase adenylyltransferase index pos1 pos2 score npdbs avgdist mindist nshort 0 294 369 9.033382 0 - - 0 638 PF00329 PF03350 50 1 9.031046 family 1, PF00329: Respiratory-chain NADH dehydrogenase, 30 Kd subunit family 2, PF03350: Uncharacterized protein family, UPF0114 index pos1 pos2 score npdbs avgdist mindist nshort 0 79 22 9.031046 0 - - 0 #639 PF00164 PF00347 276 1 9.012705 family 1, PF00164: Ribosomal protein S12 family 2, PF00347: Ribosomal protein L6 Ribosomal protein L6: structural evidence of gene index pos1 pos2 score npdbs avgdist mindist nshort 0 175 179 9.012706 0 - - 0 640 PF00281 PF00285 193 1 9.010914 family 1, PF00281: Ribosomal protein L5 family 2, PF00285: Citrate synthase index pos1 pos2 score npdbs avgdist mindist nshort 0 19 750 9.010915 0 - - 0 641 PF00573 PF08298 51 1 9.001663 family 1, PF00573: Ribosomal protein L4/L1 family Yeast ribosomal proteins L4, L17, L20, and L25 exhibit family 2, PF08298: PrkA AAA domain Cloning and characterization of the Bacillus subtilis prkA index pos1 pos2 score npdbs avgdist mindist nshort 0 52 687 9.001663 0 - - 0