Catalyst Sequence Similarity Project

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Contents

Introduction

Using strict protein alignment searches to add entities to Reactome.

  • At the 2012 SAB Bill Pearson noted that many of the catalysts entities that are currently used in Reactome events could be used to identify functional analogues. The functional analogues could then be added to a CandidateSet that a would be used in place of the original entity of the catalyst.
  • Bill pointed out that a strict identity (sequence alignment) search of 80% or better could provide a number of proteins that should probably be added to the query entity in an entity set. The "entity match" identity percentage of 80% or better, is really more of a guideline, not a strict rule (similar to the rules of piracy).
  • There were other "sorts" of identity that might be used to bolster a search that produced protein alignments that were not up to the 80% or better cut-off, such as active-site alignments plus general protein sequence similarity alignments. For sequences that share less that 80% identity he would use functional data. This second tranche would range from 40% identity or similarity or higher, but the candidate would have conserved functional sites for active site, binding, modified residues, and/or metal coordination.
    • Following our discussion with Bill at the SAB, Lisa Matthews created and sent these uniprot lists from Reactome to Bill Pearson:
    1. Simple catalyst (not part of a complex) that are unmodified.
    2. Simple catalysts that have modified residues
    3. The activeunit of catalysts that are complexes.
  • Strategy to incorporate the April 2012 Bill Pearson data into Reactome.
  • Broadly the steps would be:
    1. Enter all of the new Bill Pearson Uniprot IDs into into Reactome as CandidateSets (more about this below)
    2. A brief summation that describes the newly added UniProt IDs, a url reference to the reactome wiki page for the project, and a author [Pearson W] will be added to the CandidateSet
    3. Notify curators that changes have been made.
    4. Curators will use the google spreadsheet here to identify what catalysts have new additions . To complex, name of curator is listed on this wiki page.
    5. Curators will look over the CandidateSet and remove Uniprots IDs that they think should not be included.
    6. Curators will enter a reason that candidate Uniprot IDs were not included on the reactome wiki page for the project,
  • I (meaning Marc Gillespie) will enter all of the new Bill Pearson candidate sets.
  • Each new functional homolog is identified on the wiki page for the project. For each Reactome entity that Bill found a functional homolog for I will create a CandidateSet. If there is already a set I will add to it. The Reactome entity that Bill used initially will be the member of the set, the functional homologues that Bill identified will be the candidates.
  • The set will have Bill Pearson as the author, and a literature reference, in the form of the wiki URL that documents the project. The URL will have an anchor link that will refer back to the Reactome entity that is the founding member of the Candidate set.
  • I will also write a quick summation for the set detailing what entities were added to the set, based on Bill's analysis. This summation will provide a way for us, and our users, to track what members of the candidate set were from Bill's analysis, and allow us the freedom to add others, or accommodate other entities already identified.
  • Once all of the sets are created, we will ask curators to track down the newly created CandidateSets, using the Google spreadsheet with the catalyst reactions affected and the curator who created that catalyst reaction. If the curator removes one of the candidates, then they should document their reason on the project wiki page. This feedback is critical for the development and improvement of the process.
  • We are planning to have the annotation part done over the next two weeks, and would ask that curators make the time to complete their review by the second week of January.
  • Web Display, ie summation catenation, might also be warranted if we have time.

Q&A

Q:Will these candidateSets be different than other candidateSets in Reactome?
A:No, this is the same, or at least similar to some practices at GO. If the curator "agrees" with the creation of the CandidateSet, then the reviewing curator updates the set to include the curator as the reviewer of that record.

Could Bill look at protein families that are not in Reactome and get some 'low hanging fruit' for curation? Bijay has a list. Need some more information from Bill Pearson. The BioPAX export would not necessarily link back to a reference. We need to figure this out before we make this public. Mid-January we will check in with what the curators have done with the current list and evaluate what we should ask for in the future.

Observations

The Pearson stuff is pretty straight forward. Out of the Pearson identified sequences only about six to twenty percent are unknown to Reactome. This number varies by "biological area". For instance, Bijay's cytochromes had many, many hits, but they are mostly (95%) known to Rectome. For other areas. The likelihood of getting a new hit (unknown to Reactome), was higher.

Key

Use this key to interpret the following data

Example Output:


>O00327|538:*K l40_i: Q8WYA1 48.6% |538:559:*X:=KK


Where the query sequence was "O00327", it has functional annotations using the legend:


  • active_site: @
  • site: #
  • binding: ^
  • mod_res: *
  • metal: !


So a modified residue (*K) at residue 538.

This query matched another human protein (I do not report self-matches) called: Q8WYA1, which is 48.6%

identical (global match), and has the identical lysine (K) at residue 559. The "*X" indicates that uniprot annotates

the "*" modified site in the query O00327, but not in the library sequence Q82YA1.

There are three types of matches that can be reported:

  • l40_i library sequence is >= 40% identical and all functional residues are identical (_i)
  • l40_c library sequence is >= 40% identical and all functional residues are conserved (_c)
  • l80 no functional annotation on query, but library sequence is >=80% identical globally.

April 24, 2012

Summary

  • 110 identifiers from Reactome were matched to 284 sequences. The matches are categorized as described above.
  • 38 new EWAS were added to the database, equalling about 13% of the 284 identified sequences.
  • 7 of the 110 Reactome identifiers were matched to sequences where the curator had already created a set, the Reactome identifier was a catalyst that was not referred to my any other entity within the Reactome dataset, or the identified sequences were part of a complex. For the last category see P28062 which is part of the 26S complex already.

O00327

538:*K

l40_i:

Q8WYA1

48.6% |538:559:*X:=KK

O00445

138:!L|139:!D|145:!D|197:!D|198:!F|199:!D|202:!S|205:!D|278:*Y

l40_c:

Q8N9I0

56.0% |138:169:!!:=LL|139:170:!!:=DD|145:176:!!:=DD|197:228:!!:=DD|198:229:!!:=FF|199:230:!!:=DD|202:233:!!:=SS|203:234:X!:>RK|205:236:!!:=DD|278:309:*X:=YY

O14792

255:^Y

l40_i:

Q8IZT8

46.1% |255:293:^^:=YY

  • [Bijay] Created - Reaction involving catalyst.

O15244

451:#C

l40_i:

O15245

69.9% |451:450:##:=CC

Note: This O15244 based candidate set is the reverse of the O15245 based candidate set.

O15245

450:#C

l40_i:

O15244

69.9% |450:451:##:=CC

  • [Bijay] Created CandidateSet present in Catalyst. Note: This O15245 based candidate set is the reverse of the O15244 based candidate set.

O43174

442:!C

l40_i:

Q6V0L0

44.3% |442:459:!!:=CC

O43286

236:!D|329:!H

l40_i:

Q9UBX8

70.6% |236:230:!!:=DD|329:323:!!:=HH

O60488

89:*K

l40_i:

O95573

64.6% |89:98:*X:=KK|584:593:X*:=SS|674:683:X*:=SS|679:688:X*:=TT

O75795



l80:

P54855

94.2%

O75881

449:!C

l40_i:

P22680

40.5% |449:444:!!:=CC

O76082

486:*Y

l40_i:

Q9H015

76.5% |486:484:*X:=YY

O95573

593:*S|683:*S|688:*T

l40_i:

O60488

64.6% |98:89:X*:=KK|593:584:*X:=SS|683:674:*X:=SS|688:679:*X:=TT

P00374

10:^A|65:^N|71:^R

l40_i:

Q86XF0

92.0% |10:10:^^:=AA|65:65:^X:=NN|71:71:^^:=RR

P00568

1:*M|39:^T

l40_c:

P30085

40.8% |1:1:*#:=MM|39:34:^X:>TA|63:55:X*:=KK

P00746

66:@H|114:@D|208:@S

l40_i:

P51124

41.2% |66:66:@@:=HH|114:111:@@:=DD|208:207:@@:=SS

New EWAS

P00797

104:@D|292:@D

l40_i:

P07339

41.6% |104:97:@@:=DD|292:295:@@:=DD

P05120

380:#R

l40_i:

P35237

45.5% |380:341:##:=rR New EWAS

P50452

43.3% |380:339:##:=rR New EWAS

P05181

129:*S|437:!C



l40_i:

P33261

56.7% |129:127:*X:=SS|437:435:!!:=CC

P11712

57.1% |129:127:*X:=SS|437:435:!!:=CC

P10632

56.3% |129:127:*X:=SS|437:435:!!:=CC

P24903

47.9% |129:128:*X:=SS|437:436:!!:=CC

P20813

46.2% |129:128:**:=SS|437:436:!!:=CC

P10635

40.1% |129:135:*X:=SS|295:301:X^:=DD|437:443:!!:=CC



l40_c:

P11509

48.0% |106:107:X^:=FF|129:131:*X:=SS|295:297:X^:>DN|437:439:!!:=CC

Q16696

48.0% |129:131:*X:=SS|295:297:X^:>DN|437:439:!!:=CC

P20853

46.6% |129:131:*X:>SA|437:439:!!:=CC

Q96SQ9

40.2% |129:131:*X:>ST|437:440:!!:=CC

P06133



l80:

P16662

85.6%

O75310

85.8%

P36537

85.4%

Q9BY64

84.1% New EWAS, Though two other isoforms are annotated.

P06276

226:@S|353:@E|466:@H

l40_i:

P22303

51.3% |226:234:@@:=SS|353:365:@@:=EE|466:478:@@:=HH

P07288

65:@H|120:@D|213:@S

l40_i:

P20151

77.0% |65:65:@@:=HH|120:120:@@:=DD|213:213:@@:=Ss

P06870

60.3% |65:65:@@:=HH|120:120:@@:=DD|213:214:@@:=SS

New EWAS

Q9UKR3

41.5% |65:76:@@:=HH|120:124:@@:=DD|213:218:@@:=SS

New EWAS

P08311

64:@H|108:@D|201:@S

l40_i:

P20718

55.5% |64:64:@@:=HH|108:108:@@:=DD|201:202:@@:=SS

New EWAS

P08684

442:!C

l40_i:

P24462

88.3% |442:442:!!:=CC

P20815

84.1% |442:441:!!:=CC

Q9HB55

75.7% |442:442:!!:=CC

P0C869

335:@S|615:@D

l40_i:

Q86XP0

49.6% |335:361:@@:=SS|615:647:@@:=DD

Q68DD2

40.5% |335:395:@@:=SS|615:680:@@:=DD

Catalyst2.


P10632

435:!C

l40_i:

P33261*

78.0% |435:435:!!:=CC

P11712*

78.0% |435:435:!!:=CC

P05181*

56.3% |127:129:X*:=SS|435:437:!!:=CC

P24903*

50.1% |435:436:!!:=CC

P20813*

50.3% |127:128:X*:=SS|435:436:!!:=CC

P20853*

48.8% |435:439:!!:=CC

Q96SQ9*

42.1% |435:440:!!:=CC

P10635*

42.0% |293:301:X^:=DD|435:443:!!:=CC

l40_c:

P33260

77.1% |99:99:X*:>NS|435:435:!!:=CC

Q16696*

50.6% |293:297:X^:>DN|435:439:!!:=CC

P10635

301:^D|443:!C

l40_i:

P51589

41.8% |301:307:^X:=DD|443:448:!!:=CC

P10632

42.0% |301:293:^X:=DD|443:435:!!:=CC

Q8TAV3

40.8% |301:292:^X:=DD|443:433:!!:=CC

P05181

40.1% |135:129:X*:=SS|301:295:^X:=DD|443:437:!!:=CC

P33261

40.2% |301:293:^X:=DD|443:435:!!:=CC

P11712

40.3% |301:293:^X:=DD|443:435:!!:=CC

Catalyst2.

P11117

42:@H|287:@D

l40_i:

P15309

44.8% 41:43:X^:=RR|42:44:@@:=HH|45:47:X^:=RR|47:49:X#:=PP|109:111:X^:=RR|136:138:X#:=WW|142:144:X#:=HH|204:206:X#:=WW|286:289:X^:=HH|287:290:@@:=DD

Q9BZG2

43.4% |42:41:@@:=HH|287:289:@@:=DD

Catalyst.

P11509

107:^F|297:^N|439:!C

l40_i:

P20853

93.9% |107:107:^X:=FF|297:297:^X:=NN|439:439:!!:=CC

Q16696

93.7% |107:107:^X:=FF|297:297:^^:=NN|439:439:!!:=CC

P24903

52.7% |107:104:^X:=FF|297:294:^X:=NN|439:436:!!:=CC

l40_c:

P05181

48.0% |107:106:^X:=FF|131:129:X*:=SS|297:295:^X:>ND|439:437:!!:=CC

P11712

435:!C

l40_i:

P33261

91.2% |435:435:!!:=CC

P10632

78.0% |435:435:!!:=CC

P05181

57.1% |127:129:X*:=SS|435:437:!!:=CC

P24903

49.7% |435:436:!!:=CC

P20853

48.6% |435:439:!!:=CC

P20813

48.5% |127:128:X*:=SS|435:436:!!:=CC

Q96SQ9

43.1% |435:440:!!:=CC

P10635

40.3% |293:301:X^:=DD|435:443:!!:=CC

l40_c:

Q16696

49.7% |293:297:X^:>DN|435:439:!!:=CC

l80:

P33260

81.8%

Catalyst.

P13584

315:^E|453:!C

l40_i:

Q02928

52.4% |315:321:^^:=EE|453:457:!!:=CC

Q5TCH4

50.7% |315:321:^^:=EE|453:457:!!:=CC

P78329

43.0% |315:328:^^:=EE|453:468:!!:=CC

Q6NT55

42.2% |315:335:^^:=EE|453:475:!!:=CC

Q08477

44.3% |315:328:^^:=EE|453:468:!!:=CC

Q9HBI6

42.5% |315:328:^^:=EE|453:468:!!:=CC

Catalyst.

P13866

43:#G|300:#R

l40_i:

Q9NY91

70.2% |43:43:#X:=GG|300:300:#X:=RR

New EWAS

P31639

58.9% |43:40:##:=GG|300:300:##:=RR

Q2M3M2

54.4% |43:52:#X:=Gg|300:304:#X:=RR

P53794

44.9% |43:24:##:=GG|300:285:##:=RR

Catalyst.

P15088

176:!H|179:!E|304:!H|378:@E

l40_i:

P15086

49.5% |176:176:!!:=HH|179:179:!!:=EE|304:304:!!:=HH|378:378:@@:=EE

New EWAS

Q96IY4

40.4% |176:181:!!:=HH|179:184:!!:=EE|304:310:!!:=HH|378:385:@@:=EE

New EWAS

Catalyst.

P15538

450:!C

l40_i:

P19099

93.2% |450:450:!!:=CC

Catalyst.

P16278

188:@E|268:@E

l40_i:

Q6UWU2

52.7% |188:186:@@:=EE|268:264:@@:=EE

Catalyst.

P16870

114:!H|117:!E|248:!H|342:@E

l40_i:

P15169

45.8% |114:86:!!:=HH|117:89:!!:=EE|179:151:X@:=RR|248:216:!!:=HH|342:308:@@:=EE New EWAS

Catalyst.

P17516

50:^D|54:#L|55:@Y|75:*K|84:#K|117:^H|196:*Y|270:*K

l40_c:

Q04828

82.7% |50:50:^X:=DD|54:54:##:=LL|55:55:@@:=YY|75:75:*X:=KK|84:84:##:=KK|117:117:^^:=HH|196:196:*X:=YY|222:222:X#:>QH|270:270:*X:=KK|304:304:X^:=RR

l80:

P42330

83.9%

P52895

81.4%

Catalyst.

P17612

3:*N|11:*S|49:*T|73:^K|140:*S|167:@D|196:*T|198:*T|202:*T|339:*S

l40_c:

P22694

92.9% |3:3:**:=NN|11:11:*X:=SS|49:49:*X:=TT|69:69:X*:>HY|73:73:^^:=KK|140:140:*X:=SS|167:167:@@:=DD|196:196:*X:=TT|198:198:**:=TT|202:202:*X:=TT|267:267:X*:=KK|339:339:**:=SS

P22612

83.5% |3:3:*X:=NN|11:10:*X:>ST|49:49:*X:=TT|73:73:^^:=KK|140:140:*X:=SS|167:167:@@:=DD|196:196:*X:=TT|198:198:**:=TT|202:202:*X:=TT|339:339:**:=SS

Catalyst. In this case. The set already existed.

P19099

450:!C

l40_i:

P15538

93.2% |450:450:!!:=CC

Catalyst.

P20813

128:*S|436:!C

l40_i:

P24903

48.4% |128:128:*X:=SS|436:436:!!:=CC

P10632

50.3% |128:127:*X:=SS|436:435:!!:=CC

P11712

48.5% |128:127:*X:=SS|436:435:!!:=CC

P33261

48.1% |128:127:*X:=SS|436:435:!!:=CC

P05181

46.2% |128:129:**:=SS|436:437:!!:=CC

l40_c:

Q16696

53.2% |128:131:*X:=SS|294:297:X^:>SN|436:439:!!:=CC

P20853

51.8% |128:131:*X:>SA|436:439:!!:=CC

Q96SQ9

47.6% |128:131:*X:>ST|436:440:!!:=CC

P51589

41.7% |128:141:*X:>ST|436:448:!!:=CC

Catalyst.

P20815

441:!C

l40_i:

P08684

84.1% |441:442:!!:=CC

P24462

81.5% |441:442:!!:=CC

Q9HB55

75.5% |441:442:!!:=CC

Catalyst.

P20853

439:!C

l40_i:

P11509

93.9% |107:107:X^:=FF|297:297:X^:=NN|439:439:!!:=CC

Q16696

91.5% |297:297:X^:=NN|439:439:!!:=CC

P24903

50.3% |439:436:!!:=CC

P33261

49.4% |439:435:!!:=CC

P11712

48.6% |439:435:!!:=CC

P10632

48.8% |439:435:!!:=CC

Q96SQ9

47.6% |439:440:!!:=CC

P51589

40.7% |439:448:!!:=CC

l40_c:

P20813

51.8% |131:128:X*:>AS|439:436:!!:=CC

P05181

46.6% |131:129:X*:>AS|439:437:!!:=CC

Catalyst.

P22303

234:@S|365:@E|478:@H

l40_i:

P06276

51.3% |234:226:@@:=SS|365:353:@@:=EE|478:466:@@:=HH

Catalyst.

P22310



l80:

P35504

93.4%

P35503

93.3%

Catalyst.

P22680

444:!C

l40_i:

O75881

40.6% |444:449:!!:=CC

Catalyst.

P24462

442:!C

l40_i:

P08684

88.3% |442:442:!!:=CC

P20815

81.5% |442:441:!!:=CC

Q9HB55

71.2% |442:442:!!:=CC

Catalyst.

P24903

436:!C

l40_i:

*Q16696

52.3% |294:297:X^:=NN|436:439:!!:=CC

*P11509

52.7% |104:107:X^:=FF|294:297:X^:=NN|436:439:!!:=CC

*P20853

50.3% |436:439:!!:=CC

*P33261

51.1% |436:435:!!:=CC

*P11712

49.7% |436:435:!!:=CC

*P10632

50.1% |436:435:!!:=CC

*P05181

47.9% |128:129:X*:=SS|436:437:!!:=CC

*P20813

48.4% |128:128:X*:=SS|436:436:!!:=CC

*Q96SQ9

45.7% |436:440:!!:=CC

P51589

40.1% |436:448:!!:=CC

Catalyst.

P27361

2:*A|71:^K|166:@D|170:*S|198:*T|202:*T|204:*Y|207:*T

l80:

P28482

82.8%

Catalyst. Not released

P28062

73:@T

l40_i:

P28074

56.6% |73:60:@@:=TT|121:108:X^:=AA

A5LHX3

41.2% |73:50:@@:=TT

*Not created. All homologs are part of 26S proteosome complex already.

P28074

60:@T|108:^A

l40_i:

P28062

56.6% |60:73:@@:=TT|108:121:^X:=AA

l40_c:

A5LHX3

41.4% |60:50:@@:=TT|108:98:^X:>AS

*Not created. All homologs are part of 26S proteosome complex already.

P30085

1:#M|55:*K

l40_c:

P00568

40.8% |1:1:#*:=MM|34:39:X^:>AT|55:63:*X:=KK

Catalyst.

P31639

40:#G|300:#R

l40_i:

P13866

58.9% |40:43:##:=GG|300:300:##:=RR

Q9NY91

55.4% |40:43:#X:=GG|300:300:#X:=RR

Q2M3M2

53.2% |40:52:#X:=Gg|300:304:#X:=RR

P53794

42.8% |40:24:##:=GG|300:285:##:=RR

Catalyst.

P31749

14:*K|20:*K|53:^N|86:^R|124:*S|126:*S|129:*S|161:^F|176:*Y|179:^K|230:^A|234:^E|274:@D|292:^D|308:*T|473:*S|474:*Y

l80:

Q9Y243 82.2%

P31751

81.1%

Catalyst.

P32019

383:^E

l40_i:

Q01968

41.6% |383:278:^X:=EE

Catalyst.

P32189

20:^T|24:^R|94:^R|148:^Y|265:^D|287:^T|332:^G

l40_i:

Q14409

97.5% |20:20:^^:=TT|24:24:^^:=RR|94:94:^^:=RR|148:148:^^:=YY|265:259:^^:=DD|287:281:^^:=TT|332:326:^^:=GG New EWAS

Q14410

87.5% |20:20:^^:=TT|24:24:^^:=RR|94:94:^^:=RR|148:148:^^:=YY|265:259:^^:=DD|287:281:^^:=TT|332:326:^^:=GG New EWAS

Catalyst.

P33121

1:*M|84:*Y|543:*K|632:*K

l40_c:

Q9UKU0

66.9% |1:1:*X:=MM|84:84:*X:>YH|543:543:*X:=KK|632:632:*X:=KK

Catalyst.

P33176

2:*A|166:*K|933:*S

l40_i:

O60282

75.0% |2:2:*X:=AA|166:167:*X:=KK|336:338:X*:=TT|795:797:X*:=TT|933:935:*X:=SS

Q12840

66.2% |2:2:**:=AA|166:167:*X:=KK|933:931:*X:=SS

Catalyst.

P33260

99:*S|435:!C

l40_c:

P10632

77.1% |99:99:*X:>SN|435:435:!!:=CC

Q96SQ9

42.5% |99:103:*X:>ST|435:440:!!:=CC

l80:

P11712

81.8%

P33261

81.0%

Catalyst.

P33261

435:!C

l40_i:

P11712

91.2% |435:435:!!:=CC

P10632

78.0% |435:435:!!:=CC

P05181

56.7% |127:129:X*:=SS|435:437:!!:=CC

P24903

51.1% |435:436:!!:=CC

P20853

49.4% |435:439:!!:=CC

P20813

48.1% |127:128:X*:=SS|435:436:!!:=CC

Q96SQ9

43.5% |435:440:!!:=CC

P10635

40.2% |293:301:X^:=DD|435:443:!!:=CC

l40_c:

Q16696

50.9% |293:297:X^:>DN|435:439:!!:=CC

l80:

P33260

81.0%

Catalyst.

P37058

185:^S|198:@Y

l40_i:

Q53GQ0

40.8% |185:189:^^:=SS|198:202:@@:=YY

Catalyst.

P40306

40:@T

l40_i:

Q99436

56.3% |40:44:@@:=TT|150:154:X*:=YY

  • NOTE Did not create anything here. This is captured in the annotation of the 26S 26S proteosome.

P48029

620:*T

l40_c:

P48066

51.8% |620:623:*X:>TA

P48065

51.1% |620:599:*X:>TS

Q99884

41.8% |620:596:*X:>TA

Catalyst.

P48730

38:^K|128:@D|328:*S|329:*T|331:*S|337:*T|344:*T|347:*T|349:*T|350:*S|352:*T|355:*T|356:*S|361:*S|382:*S|383:*S|384:*S|387:*T|392:*T|393:*S|396:*S|397:*T|398:*S|406:*S|407:*S|411:*S

l80:

P49674

82.0%

  • Note: Did not Create CandidateSet. This was already present in

CandidateSet.

P49674

38:^K|128:@D|323:*S|343:*S|350:*S|351:*T|354:*S|362:*T|363:*S|389:*S|391:*S|405:*S|407:*T|408:*S

l80:

P48730

82.0%

Catalyst.

P49961

49:*Y|65:*Y|174:@E

l40_c:

Q5MY95

43.4% |49:43:*X:>YF|65:59:*X:=YY|174:168:@@:=Ee New EWAS

Catalyst.

P51451

269:^K|360:@D|389:*Y

l40_i:

Q9H3Y6

40.5% |269:258:^^:=KK|272:261:X*:=KK|360:350:@@:=DD|389:380:**:=YY New EWAS

Catalyst.

P51589

448:!C

l40_i:

P20853

40.5% |448:439:!!:=CC

P10635

41.8% |307:301:X^:=DD|448:443:!!:=CC

P24903

40.1% |448:436:!!:=CC

l40_c:

Q16696

40.8% |307:297:X^:>DN|448:439:!!:=CC

P20813

41.7% |141:128:X*:>TS|448:436:!!:=CC

Catalyst.

P53794

24:#G|285:#R

l40_i:

Q2M3M2

45.1% |24:52:#X:=Gg|285:304:#X:=RR

P13866

44.9% |24:43:##:=GG|285:300:##:=RR

P31639

42.8% |24:40:##:=GG|285:300:##:=RR

Q9NY91

40.5% |24:43:#X:=GG|285:300:#X:=RR

Catalyst.

P54317

171:@S|195:@D|206:!E|209:!R|211:!D|214:!D|282:@H

l40_i:

P16233

64.0% |171:169:@@:=SS|195:193:@@:=DD|206:204:!X:=EE|209:207:!X:=RR|211:209:!X:=DD|214:212:!X:=DD|282:280:@@:=HH

P54315

62.7% |171:171:@X:=SS|195:194:@X:=DD|206:205:!!:=EE|209:208:!!:=RR|211:210:!!:=DD|214:213:!!:=DD|282:281:@X:=HH New EWAS

Catalyst.

P63027

2:*S|75:*S

l40_i:

P23763

78.3% |2:2:*X:=SS|61:63:X*:=SS|75:77:*X:=SS

Q15836

67.8% |2:2:*X:=SS|61:44:X*:=SS|75:58:**:=SS

  • Note: Did not create set, Vamps are generally thought not to be substitutable.

P68104

29:*Y|36:*K|41:*K|44:*K|55:*K|79:*K|86:*Y|141:*Y|146:*K|162:*Y|165:*K|172:*K|179:*K|255:*K|301:*E|318:*K|374:*E|392:*K|395:*K|432:*T|439:*K

l40_i:

Q5VTE0

99.6% |29:29:**:=YY|36:36:**:=KK|41:41:*X:=KK|44:44:*X:=KK|55:55:**:=KK|79:79:**:=KK|86:86:**:=YY|141:141:**:=YY|146:146:*X:=KK|162:162:**:=YY|165:165:**:=KK|172:172:*X:=KK|179:179:*X:=KK|254:254:X*:=YY|255:255:*X:=KK|301:301:**:=EE|318:318:**:=KK|374:374:**:=EE|392:392:*X:=KK|395:395:*X:=KK|432:432:*X:=TT|439:439:*X:=kk New EWAS

Q05639

92.4% |29:29:**:=YY|36:36:*X:=KK|41:41:*X:=KK|44:44:*X:=KK|55:55:**:=KK|79:79:*X:=KK|86:86:*X:=YY|141:141:**:=YY|146:146:*X:=KK|162:162:*X:=YY|165:165:**:=KK|172:172:*X:=KK|179:179:**:=KK|255:255:*X:=KK|301:301:**:=EE|318:318:*X:=KK|374:374:**:=EE|392:392:*X:=KK|395:395:*X:=KK|432:432:*X:=TT|439:439:**:=kK New EWAS

Catalyst.

P78329

328:^E|468:!C

l40_i:

Q08477

87.9% |328:328:^^:=EE|468:468:!!:=CC

This entity was already with P78329 in a defined set for the reaction. Changed the defined set to a candidate set, but kept P78329 as Q08477 members of that new candidate set.

Q9HBI6

86.3% |328:328:^^:=EE|468:468:!!:=CC

Q6NT55

64.5% |328:335:^^:=EE|468:475:!!:=CC

Q02928

44.2% |328:321:^^:=EE|468:457:!!:=CC

P13584

43.3% |328:315:^^:=EE|468:453:!!:=CC

Q5TCH4

43.2% |328:321:^^:=EE|468:457:!!:=CC ===l80: Q===9HCS2 81.1%

P98187

81.2%

Catalyst.

P98187

468:!C

l40_i:

Q9HCS2

77.7% |468:468:!!:=CC

l80:

P78329

81.2%

Catalyst.

Q02928

321:^E|457:!C

l40_i:

Q5TCH4

94.8% |321:321:^^:=EE|457:457:!!:=CC

P13584

52.4% |321:315:^^:=EE|457:453:!!:=CC

Q08477

44.7% |321:328:^^:=EE|457:468:!!:=CC

P78329

44.2% |321:328:^^:=EE|457:468:!!:=CC

Q9HBI6

44.6% |321:328:^^:=EE|457:468:!!:=CC

Q6NT55

42.8% |321:335:^^:=EE|457:475:!!:=CC

Catalyst.

Q08477

328:^E|468:!C

l40_i:

P78329

87.9% |328:328:^^:=EE|468:468:!!:=CC

Q9HBI6

82.3% |328:328:^^:=EE|468:468:!!:=CC

Q6NT55

64.4% |328:335:^^:=EE|468:475:!!:=CC

Q02928

44.7% |328:321:^^:=EE|468:457:!!:=CC

Q5TCH4

43.0% |328:321:^^:=EE|468:457:!!:=CC

P13584

44.2% |328:315:^^:=EE|468:453:!!:=CC

Catalyst.

Q12794

131:@E

l40_i:

O43820

41.1% |131:129:@@:=EE New EWAS

Catalyst.

Q12908

328:#N

l40_c:

Q3KNW5

42.9% |328:335:#X:>NS

Catalyst.

Q13219

562:!H|563:@E|566:!H|572:!H

l40_i:

Q9BXP8

41.4% |562:733:!!:=HH|563:734:@@:=EE|566:737:!!:=HH|572:743:!!:=HH

Catalyst.

Q13547

74:*K|141:@H|220:*K|221:*Y|393:*S|406:*S|421:*S|423:*S|432:*K

l40_c:

Q92769

85.5% |74:75:**:=KK|89:90:X*:=KK|141:142:@@:=HH|220:221:*X:=KK|221:222:*X:=YY|261:262:X*:=CC|273:274:X*:=CC|393:394:**:=ss|406:407:**:=SS|421:422:**:=ss|423:424:**:=ss|432:433:*X:>KR

  • Note: Did not create anything here. These are both present in complex.

Q14542

252:*S

l40_c:

Q99808

46.8% |237:254:X*:>TS|252:272:*X:>SN

Catalyst.

Q16647

441:!C

l40_i:

Q9UNU6

41.1% |441:440:!!:=CC

Catalyst.

Q16696

297:^N|439:!C

l40_i:

P11509

93.7% |107:107:X^:=FF|297:297:^^:=NN|439:439:!!:=CC

P20853

91.5% |297:297:^X:=NN|439:439:!!:=CC

P24903

52.3% |297:294:^X:=NN|439:436:!!:=CC

l40_c:

P20813

53.2% |131:128:X*:=SS|297:294:^X:>NS|439:436:!!:=CC

P33261

50.9% |297:293:^X:>ND|439:435:!!:=CC

P11712

49.7% |297:293:^X:>ND|439:435:!!:=CC

P10632

50.6% |297:293:^X:>ND|439:435:!!:=CC

P05181

48.0% |131:129:X*:=SS|297:295:^X:>ND|439:437:!!:=CC

P51589

40.8% |297:307:^X:>ND|439:448:!!:=CC

Catalyst.

Q53GQ0

189:^S|202:@Y

l40_i:

P37058

40.8% |189:185:^^:=SS|202:198:@@:=YY

Catalyst.

Q658P3

17:*S|20:*S|36:^S|38:^D|39:^F|58:^S|59:^R|91:^V|116:^N|151:^A|316:!H|409:!H

l40_c:

Q8NFT2

52.2% |17:9:*X:=SS|20:12:*X:=SS|36:38:^X:=SS|38:40:^X:=DD|39:41:^X:=FF|58:60:^X:=SS|59:61:^X:=RR|91:93:^X:>VI|116:118:^X:=NN|151:151:^X:=AA|316:316:!!:=HH|409:409:!!:=HH New EWAS

Catalyst.

Q68CK6

139:^Q|364:^T|446:^D|461:^R|472:^R|501:^R|532:^K|557:^K

l40_i:

Q08AH3

97.2% |139:139:^^:=QQ|364:364:^^:=TT|446:446:^^:=DD|461:461:^^:=RR|472:472:^^:=RR|501:501:^^:=RR|532:532:^^:=KK|557:557:^^:=KK New EWAS

P0C7M7

57.0% |139:147:^X:=QQ|364:373:^X:=TT|446:455:^^:=DD|461:470:^^:=RR|472:481:^X:=RR|501:510:^X:=RR|532:541:^X:=KK|538:547:X*:=YY|557:566:^^:=KK

l40_c: New EWAS

Q6NUN0

53.1% |139:148:^X:=QQ|364:373:^X:>TS|446:455:^^:=DD|461:470:^^:=RR|472:481:^X:=RR|501:510:^X:=RR|532:541:^X:=KK|557:566:^^:=KK New EWAS


Catalyst.

Q6IB77

20:*K

l40_i:

Q8WU03

40.8% |20:19:*X:=KK New EWAS



l40_c:

Q969I3

41.0% |20:19:*X:>KR New EWAS

Catalyst.

Q6V0L0

459:!C

l40_i:

O43174

44.3% |459:442:!!:=CC

Catalyst.

Q6XPS3

320:@C

l40_i:

P56180

83.3% |320:338:@@:=CC New EWAS

Catalyst.

Q8TAV3

433:!C

l40_i:

P10635

40.8% |292:301:X^:=DD|433:443:!!:=CC

Catalyst.

Q92581

625:*S

l40_i:

Q96T83

63.8% |625:695:**:=SS

Q8IVB4

54.2% |625:612:*X:=SS

Catalyst.

Q92781

163:^S|175:@Y

l40_i:

O75452

52.2% |163:164:^^:=SS|175:176:@@:=YY New EWAS

O14756

51.2% |163:164:^^:=SS|175:176:@@:=YY New EWAS

Q8NEX9

47.7% |163:160:^^:=SS|175:172:@@:=YY New EWAS

Q9BPW9

45.3% |82:83:X^:=DD|163:164:^^:=SS|175:176:@@:=YY|179:180:X^:=KK New EWAS

Catalyst.

Q92831

40:*S|729:*Y|733:*K

l40_c:

Q92830

70.1% |40:49:*X:>sa|729:734:**:=YY|733:738:*X:=KK

Catalyst.

Q96HE7

187:^R|189:^T|200:^W|252:^S|255:^H|287:^R

l40_i:

Q86YB8

60.0% |187:186:^^:=RR|189:188:^^:=TT|200:199:^^:=WW|252:251:^^:=SS|255:254:^^:=HH|287:286:^^:=RR New EWAS

Catalyst.

Q99436

44:@T|154:*Y

l40_i:

P40306

56.3% |44:40:@@:=TT|154:150:*X:=YY

  • [?] Did not Create a CandidateSet] as the

Catalyst is not referred to by any other entity.

Q99726

38:*S

l40_c:

Q9BRI3

40.7% |38:28:*X:>sA

Catalyst.

Q99808

254:*S

l40_c:

Q14542

46.8% |254:237:*X:>ST|272:252:X*:>NS

Catalyst.

Q9C0K1

288:*S

l40_c:

Q15043

47.6% |288:321:*X:>SA

Catalyst.

Q9HAU4

716:@C

l40_i:

Q9HCE7

72.1% |716:725:@@:=CC

  • Did not create as Q9HAU4 is not used as a catalyst in a released reaction.

Q9HBI6

328:^E|468:!C

l40_i:

P78329

86.3% |328:328:^^:=EE|468:468:!!:=CC

Q08477

82.3% |328:328:^^:=EE|468:468:!!:=CC

Q6NT55

63.3% |328:335:^^:=EE|468:475:!!:=CC

Q02928

44.5% |328:321:^^:=EE|468:457:!!:=CC

P13584

42.3% |328:315:^^:=EE|468:453:!!:=CC

Q5TCH4

42.4% |328:321:^^:=EE|468:457:!!:=CC ===l80: Q===9HCS2 82.8%

Catalyst.

Q9HCS2

468:!C

l40_i:

P98187

77.7% |468:468:!!:=CC ===l80: Q===9HBI6 82.8%

P78329

81.1%

Catalyst.

Q9NR71

354:@S

l40_i:

P0C7U2

78.6% |354:196:@@:=SS New EWAS

Catalyst.

Q9NYR8

142:^S|155:@Y

l40_i:

P14061

43.0% |66:66:X^:=DD|142:143:^^:=SS|155:156:@@:=YY|159:160:X^:=KK

Catalyst1 and Catalyst2.

Q9NZ01

22:*K|116:*K

l40_i:

Q5HYJ1

43.7% |22:78:*X:=KK|116:172:*X:=KK New EWAS

Catalyst.

Q9UH73

163:#R|172:#N

l40_i:

Q9H4W6

89.3% |163:163:##:=RR|172:172:##:=NN

Q9HAK2

76.9% |163:162:##:=RR|172:171:##:=NN

Q9BQW3

72.0% |163:164:##:=RR|172:173:##:=NN

  • [Bruce] Did not create a CandidateSet for

Catalyst, as the catalyst was not used in any reaction.

Q9UKX2

130:*K

l40_i:

P12882

94.8% |130:130:**:=KK|1930:1928:X*:=SS|1935:1933:X*:=TT

P13535

92.6% |130:132:**:=KK|954:951:X*:=SS|1205:1202:X*:=SS

P11055

84.4% |130:130:**:=KK

Q9UKX3

81.5% |130:130:**:=KK New EWAS

P12883

81.1% |130:129:**:=KK|1043:1037:X*:=SS

P13533

80.3% |130:129:**:=KK

A7E2Y1

67.5% |130:128:*X:=KK

l40_c:

Q9Y2K3

59.2% |130:147:**:=KK|721:727:X*:=YY|1119:1125:X*:>aT ===l80: Q===9Y623 91.9% New EWAS

Catalyst.

Q9UMW8

64:@C|318:@H

l40_i:

Q3LFD5

82.4% |64:64:@@:=CC|318:318:@@:=HH New EWAS

Catalyst.

Q9UNU6

440:!C

l40_i:

Q16647

41.1% |440:441:!!:=CC

Catalyst.

Q9Y623

130:*K|1464:*Y|1478:*S|1480:*S|1482:*S|1483:*T

l40_i:

P13535

90.3% |130:132:**:=KK|952:951:X*:=SS|1203:1202:X*:=SS|1464:1463:*X:=YY|1478:1477:*X:=SS|1480:1479:*X:=SS|1482:1481:*X:=SS|1483:1482:*X:=TT

l40_c:

P12883

80.7% |130:129:**:=KK|1041:1037:X*:=SS|1464:1460:*X:=Yy|1478:1474:*X:>SA|1480:1476:*X:=SS|1482:1478:*X:=SS|1483:1479:*X:=TT

P13533

80.3% |130:129:**:=KK|1464:1462:*X:=Yy|1478:1476:*X:>SA|1480:1478:*X:=SS|1482:1480:*X:=SS|1483:1481:*X:=TT

l80:

P12882

94.1%

Q9UKX2

91.9%

P11055

83.1%

Q9UKX3

81.3%

Catalyst.

P05121

369:#R

l40_i:

P07093

40.1% |369:365:##:=RR New EWAS

Catalyst1 and Catalyst2.

P22694

3:*N|69:*Y|73:^K|167:@D|198:*T|267:*K|339:*S

l40_c:

P17612

92.9% |3:3:**:=NN|11:11:X*:=SS|49:49:X*:=TT|69:69:*X:>YH|73:73:^^:=KK|140:140:X*:=SS|167:167:@@:=DD|196:196:X*:=TT|198:198:**:=TT|202:202:X*:=TT|267:267:*X:=KK|339:339:**:=SS

P22612

79.3% |3:3:*X:=NN|69:69:*X:>YH|73:73:^^:=KK|167:167:@@:=DD|198:198:**:=TT|267:267:*X:=KK|339:339:**:=SS


Catalyst1 and Catalyst2.


P25774

139:@C|278:@H|298:@N

l40_i:

O60911

49.7% |139:138:@@:=CC|278:277:@@:=HH|298:301:@@:=NN

P07711

48.2% |139:138:@@:=CC|278:276:@@:=HH|298:300:@@:=NN

Catalyst1 and Catalyst2.