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Dataset S1: List of PKS Pathways, abbreviations, and data sources
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To accompany:
The Origins of Specificity in Polyketide Synthase Protein Interactions
Mukund Thattai, Yoram Burak, Boris I. Shraiman


The data are formatted as follows:

ABBREV      <5-letter abbreviation, sequence range (see below)>
NAME        <Polyketide product name>
AUTHOR      <First author of referenced article>
REFERENCE   <Journal name, volume, page, year of publication>
SPECIES     <Species from which the sequences were obtained>
GENES       <Standard gene names in pathway order>
ORDER       <Gene order on chromosome (see below)>

We use a sequential naming convention for all proteins in our dataset: a five-letter pathway code, followed by a three-digit sequence position code. For example, ampho_003 represents protein 3 of the amphotericin PKS. Comparison with the GENES entry allows the standard gene name to be traced.

The ORDER entry contains information about the direction of transcription (represented by the symbols '>' and '<'), as well as information about gaps in the gene cluster (represented by the symbol 'x'). For example, the Avermectin PKS entry contains the following information:

GENES	aveA1; aveA2; aveA3; aveA4;
ORDER	001>002>x003<004<

This indicates that the genes aveA1 and aveA2 are transcribed left-to-right ('>'), while genes aveA3 and aveA4 are transcribed right to left ('<'). Furthermore, the region between aveA2 and aveA3 contains genes not listed here, and is designated as a gap ('x').

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ABBREV      ampho 001-006
NAME        Amphotericin
AUTHOR      Caffrey
REFERENCE   Chem. Biol. 8 (7), 713-723 (2001)
SPECIES     Streptomyces nodosus 
GENES       amphA; amphB; amphC; amphI; amphJ; amphK;
ORDER       004>005>006>x001>002>003>

ABBREV      ansam 001-004
NAME        Ansamitocin
AUTHOR      Yu
REFERENCE   Proc. Natl. Acad. Sci. U.S.A. 99 (12), 7968-7973 (2002)
SPECIES     Streptomyces halstedii
GENES       asmA; asmB; asmC; asmD; 
ORDER       003>004>x001>002>

ABBREV      ascom 001-003
NAME        Ascomycin
AUTHOR      Wu
REFERENCE   Gene 251 (1), 81-90 (2000)
SPECIES     Streptomyces hygroscopicus
GENES       fkbB; fkbC; fkbA;
ORDER       002<001<x003>

ABBREV      aureo 001-003
NAME        Aureothin 
AUTHOR      He
REFERENCE   Chem. Biol. 10 (12), 1225-1232 (2003)
SPECIES     Streptomyces thioluteus
GENES       aurA; aurB; aurC;
ORDER       001>x002>003>

ABBREV      averm 001-004
NAME        Avermectin
AUTHOR      Ikeda
REFERENCE   Proc. Natl. Acad. Sci. USA 96, 9509-9514 (1999)
SPECIES     Streptomyces avermitilis
GENES       aveA1; aveA2; aveA3; aveA4;
ORDER       001>002>x003<004<

ABBREV      borre 001-006
NAME        Borrelidin
AUTHOR      Olano
REFERENCE   Chem. Biol. 11 (1), 87-97 (2004)
SPECIES     Streptomyces parvulus Tu4055
GENES       borA1; borA2; borA3; borA4; borA5; borA6;
ORDER       001>002>003>004>005>006>

ABBREV      chalc 001-005
NAME        Chalcomycin
AUTHOR      Ward
REFERENCE   Antimicrob. Agents Chemother. 48 (12), 4703-4712 (2004)
SPECIES     Streptomyces bikiniensis
GENES       ChmGI; ChmGII; ChmGIII; ChmGIV; ChmGV;
ORDER       001>002>003>004>005>

ABBREV      conca 001-006
NAME        Concanomycin
AUTHOR      Haydock
REFERENCE   Microbiology (Reading, Engl.) 151 (PT 10), 3161-3169 (2005)
SPECIES     Streptomyces neyagawaensis
GENES       conA; conB; conC; conD; conE; conF;
ORDER       001>002>003>004>005>006>

ABBREV      curac 001-014
NAME        Curacin
AUTHOR      Chang
REFERENCE   J. Nat. Prod. 67 (8), 1356-1367 (2004)
SPECIES     Lyngbya majuscula
GENES       curA; curB; curC; curD; curE; curF; curG; curH; curI; curJ; curK; curL; curM; curN;
ORDER       001>002>003>004>005>006>006>007>008>009>010>011>012>013>014>

ABBREV      cysto 001-006
NAME        Cystothiazole A
AUTHOR      Feng
REFERENCE   Biosci. Biotechnol. Biochem. 69 (7), 1372-1380 (2005)
SPECIES     Cystobacter fuscus
GENES       ctaB; ctaC; ctaD; ctaE; ctaF; ctaG;
ORDER       004>005>006>x001>002>003>

ABBREV      eco02 001-009
NAME        ECO-02301
AUTHOR      McAlpine
REFERENCE   J. Nat. Prod. 68 (4), 493-496 (2005)
SPECIES     Streptomyces aizunensis
GENES       Orf9; Orf10; Orf11; Orf12; Orf13; Orf14; Orf15; Orf16; Orf17;
ORDER       001>002>003>004>005>006>007>008>009

ABBREV      epoth 001-006
NAME        Epothilone
AUTHOR      Tang
REFERENCE   Science 287 (5453), 640-642 (2000)
SPECIES     Sorangium cellulosum
GENES       epoA; epoB; epoC; epoD; epoE; epoF;
ORDER       001>002>003>004>005>006>

ABBREV      eryta 001-003
NAME        Erythromycin A
AUTHOR      Brikun
REFERENCE   J. Ind. Microbiol. Biotechnol. 31 (7), 335-344 (2004)
SPECIES     Aeromicrobium erythreum
GENES       eryAI; eryAII; eryAIII;
ORDER       001>002>003>

ABBREV      eryth 001-003
NAME        Erythromycin
AUTHOR      Cortes
REFERENCE   Nature 348 (6297), 176-178 (1990)
SPECIES     Saccharopolyspora erythraea
GENES       eryAI; eryAII; eryAIII;
ORDER       001>002>003>

ABBREV      fr008 001-006
NAME        FR-008
AUTHOR      Chen
REFERENCE   Chem. Biol. 10 (11), 1065-1076 (2003)
SPECIES     Streptomyces sp. FR-008
GENES       fscA; fscB; fscC; fscD; fscE; fscF;
ORDER       004>005>006>002>003>x001<

ABBREV      gelda 001-003
NAME        Geldanamycin
AUTHOR      Rascher
REFERENCE   FEMS Microbiol. Lett. 218 (2), 223-230 (2003)
SPECIES     Streptomyces hygroscopicus NRRL 3602
GENES       gdmA1; gdmA2; gdmA3;
ORDER       001>002>003>

ABBREV      herbi 001-003
NAME        Herbimycin
AUTHOR      Rascher
REFERENCE   Appl. Environ. Microbiol. 71 (8), 4862-4871 (2005)
SPECIES     Streptomyces hygroscopicus
GENES       hbmAI; hbmAII; hbmAIII;
ORDER       001>002>003>

ABBREV      hygro 001-004
NAME        Uncharacterized
AUTHOR      Ruan
REFERENCE   Gene 203 (1), 1-9 (1997)
SPECIES     Streptomyces hygroscopicus ATCC 29253
GENES       Orf1; Orf2; Orf3; Orf4;
ORDER       001>002>003>004>

ABBREV      jamai 001-012
NAME        Jamaicamide A
AUTHOR      Edwards
REFERENCE   Chem. Biol. 11 (6), 817-833 (2004)
SPECIES     Lyngbya majuscula
GENES       jamA; jamC; jamE; jamF; jamJ; jamK; jamL; jamM; jamN; jamO; jamP; jamQ;
ORDER       001>x002>x003>004>x005>006>007>008>009>010>011>012<

ABBREV      lanka 001-002
NAME        Lankamycin
AUTHOR      Suwa
REFERENCE   Gene 246 (1-2), 123-131 (2000)
SPECIES     Streptomyces rochei
GENES       lamAI; lkmAII;
ORDER       001>x002>

ABBREV      megal 001-003
NAME        Megalomicin
AUTHOR      Volchegursky
REFERENCE   Mol. Microbiol. 37 (4), 752-762 (2000)
SPECIES     Micromonospora megalomicea
GENES       megAI; megAII; megAIII;
ORDER       001>002>003>

ABBREV      melit 001-006
NAME        Melithiazol
AUTHOR      Weinig
REFERENCE   Chem. Biol. 10 (10), 939-952 (2003)
SPECIES     Melittangium lichenicola
GENES       melB; melC; melD; melE; melF; melG;
ORDER       001>002>003>004>005>006

ABBREV      monen 001-008
NAME        Monensin
AUTHOR      Oliynyk
REFERENCE   Mol. Microbiol. 49 (5), 1179-1190 (2003)
SPECIES     Streptomyces cinnamonensis
GENES       monAI; monAII; monAIII; monAIV; monAV; monAVI; monAVII; monAVIII;
ORDER       001>002>003>004>005>006>x007<008<

ABBREV      mycin 001-005
NAME        Mycinamicin
AUTHOR      Anzai
REFERENCE   FEMS Microbiol. Lett. 218 (1), 135-141 (2003)
SPECIES     Micromonospora griseorubida
GENES       mycAI; mycAII; mycAIII; mycAIV; mycAV;
ORDER       001>002>003>004>005>

ABBREV      mycol 001-002
NAME        Mycolactone
AUTHOR      Stinear
REFERENCE   Proc. Natl. Acad. Sci. U.S.A. 101 (5), 1345-1349 (2004)
SPECIES     Mycobacterium ulcerans
GENES       mlsA1; mlsA2;
ORDER       001>002>

ABBREV      myxal 001-006
NAME        Myxalamide
AUTHOR      Silakowski
REFERENCE   Chem. Biol. 8 (1), 59-69 (2001)
SPECIES     Stigmatella aurantiaca
GENES       mxaF; mxaE; mxaD; mxaC; mxaB1; mxaB2;
ORDER       001>002>003>004>005>006>

ABBREV      myxot 001-006
NAME        Myxothiazol
AUTHOR      Silakowski
REFERENCE   J. Biol. Chem. 274 (52), 37391-37399 (1999)
SPECIES     Stigmatella aurantiaca
GENES       mtaB; mtaC; mtaD; mtaE; mtaF; mtaG;
ORDER       001>002>003>004>005>006>

ABBREV      nanch 001-011
NAME        Nanchangmycin
AUTHOR      Sun
REFERENCE   Chem. Biol. 10, 431-441 (2003)
SPECIES     Streptomyces nanchangensis NS3226
GENES       nanA1; nanA2; nanA3; nanA4; nanA5; nanA6; nanA7; nanA8; nanA9; nanA10; nanA11;
ORDER       001>002>003>004>005>006>x007<x010<x009<011<008<

ABBREV      nidda 001-005
NAME        Niddamycin
AUTHOR      Kakavas
REFERENCE   J. Bacteriol. 179 (23), 7515-7522 (1997)
SPECIES     Streptomyces caelestis
GENES       nidA1; nidA2; nidA3; nidA4; nidA5;
ORDER       001>002>003>004>005>

ABBREV      nysta 001-006
NAME        Nystatin
AUTHOR      Brautaset
REFERENCE   Chem. Biol. 7 (6), 395-403 (2000)
SPECIES     Streptomyces noursei ATCC 11455
GENES       nysA; nysB; nysC; nysI; nysJ; nysK;
ORDER       004>005>006>x001>002>003>

ABBREV      olean 001-003
NAME        Oleandomycin
AUTHOR      Shah
REFERENCE   J. Antibiot. 53 (5), 502-508 (2000)
SPECIES     Saccharopolyspora erythraea
GENES       oleAI; oleAII; OrfB;
ORDER       001>002>x003>

ABBREV      phosl 001-006
NAME        Phoslactomycin
AUTHOR      Palaniappan
REFERENCE   J. Biol. Chem. 278 (37), 35552-35557 (2003)
SPECIES     Streptomyces sp. HK803
GENES       plm1; plm2-3; plm4; plm5; plm6; plm7;
ORDER       003>004>005>006>x001>002>

ABBREV      pikro 001-005
NAME        Pikromycin
AUTHOR      Xue
REFERENCE   Proc. Natl. Acad. Sci. U.S.A. 95 (21), 12111-12116 (1998)
SPECIES     Streptomyces venezuelae
GENES       pikAI; pikAII; pikAIII; pikAIV; pikAV;
ORDER       001>002>003>004>005>

ABBREV      pimar 001-005
NAME        Pimaricin
AUTHOR      Aparicio
REFERENCE   Chem. Biol. 7 (11), 895-905 (2000)
SPECIES     Streptomyces natalensis
GENES       pimS0; pimS1; pimS2; pimS3; pimS4;
ORDER       002>001<x003>004>005>

ABBREV      rapam 001-003
NAME        Rapamycin
AUTHOR      Schwecke
REFERENCE   Proc. Natl. Acad. Sci. U.S.A. 92 (17), 7839-7843 (1995)
SPECIES     Streptomyces hygroscopicus
GENES       rapA; rapB; rapC;
ORDER       003<x001>002>

ABBREV      rifaB 001-005
NAME        Rifamycin B
AUTHOR      Schupp
REFERENCE   FEMS Microbiol. Lett. 159, 201-207 (1998)
SPECIES     Amycolatopsis mediterranei
GENES       Orf1; Orf2; Orf3; Orf4; Orf5;
ORDER       001>002>003>004>005>

ABBREV      rifam 001-005
NAME        Rifamycin
AUTHOR      Yu
REFERENCE   J. Biol. Chem. 276 (16), 12546-12555 (2001)
SPECIES     Amycolatopsis mediterranei
GENES       rifA; rifB; rifC; rifD; rifE;
ORDER       001>002>003>004>005>

ABBREV      sorap 001-002
NAME        Soraphen
AUTHOR      Ligon
REFERENCE   Gene 285 (1-2), 257-267 (2002)
SPECIES     Sorangium cellulosum
GENES       sorA; sorB;
ORDER       001>002>

ABBREV      spino 001-005
NAME        Spinosad
AUTHOR      Waldron
REFERENCE   Chem. Biol. 8 (5), 487-499 (2001)
SPECIES     Saccharopolyspora spinosa
GENES       spnA; spnB; spnC; spnD; spnE;
ORDER       001>002>003>004>005>

ABBREV      stigm 001-009
NAME        Stigmatellin
AUTHOR      Gaitatzis
REFERENCE   J. Biol. Chem. 277(15), 13082-13090 (2002)
SPECIES     Stigmatella aurantiaca
GENES       stiA; stiB; stiC; stiD; stiE; stiF; stiG; stiH; stiJ;
ORDER       001>002>003>004>005>006>007>008>009>

ABBREV      tylac 001-005
NAME        Tylactone
AUTHOR      
REFERENCE   Unpublished
SPECIES     Streptomyces fradiae
GENES       Orf1; Orf2; Orf3; Orf4; Orf5;
ORDER       001>002>003>004>005>

ABBREV      vicen 001-004
NAME        Vicenistatin
AUTHOR      Ogasawara
REFERENCE   Chem. Biol. 11 (1), 79-86 (2004)
SPECIES     Streptomyces halstedii
GENES       vinP1; vinP2; vinP3; vinP4;
ORDER       002>003>004>x001>

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