Team:Heidelberg/Templates/NRPS-W-23

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(Created page with "== SBOL and GenBank == Proper output of the designed NRPS as well as the primers, was created both for GenBank and for SBOL. Moreover the tool internal communication was shifted ...")
 
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== SBOL and GenBank ==
== SBOL and GenBank ==
Proper output of the designed NRPS as well as the primers, was created both for GenBank and for SBOL. Moreover the tool internal communication was shifted to SBOL.
Proper output of the designed NRPS as well as the primers, was created both for GenBank and for SBOL. Moreover the tool internal communication was shifted to SBOL.

Latest revision as of 03:21, 29 October 2013

SBOL and GenBank

Proper output of the designed NRPS as well as the primers, was created both for GenBank and for SBOL. Moreover the tool internal communication was shifted to SBOL.

Database Curation

The final state of the database after a major portion of SBSPKS was curated is displayed in the table below.

PathwayGeneModuleSBSPKS domainsHMM domainsSpecificity (Chirality C, TE)Specificity (CA Substrate)SBSPKSSVM (0)Stachelhaus (0)Minowa (1)LiteratureModificationsE-domain containedLiterature referencesComment
ActinomycinacmA1AA-4-MHA4-MHAhydrophobic/alphaticPIP4-MHA4-MHA-http://www.ncbi.nlm.nih.gov/pubmed/9573200"T-domain after A is definitely missing C-starter can go with or without 4-MHA"
acmB2C-A-TCSt-A-T-/4-MHAThrThrThrThrThrThr-
3C-A-T-EC-A-T-E-comLValD-ValValValValVal-X
acmC4C-A-Tcom-C-A-TDProProProProProPro-
5C-A-M-TC-A-NM-TLGlyGlyGlyGlyGlyGlyN-Methylierung
6C-A-M-T-TEC-A-NM-T-TEL, LValValValValValValN-Methylierung
ACVacvA1A-TA-T-AadAadAadAadAadAad-"A: http://www.ncbi.nlm.nih.gov/pubmed/9266851
E: http://www.ncbi.nlm.nih.gov/pubmed/21889568
TE: http://www.ncbi.nlm.nih.gov/pubmed/10715209 "
2C-A-TC-A-TD (pred) / L (sbspks, lit)CysCysCysCysCysCys-
3C-A-T-E-TEC-A-T-E-TEL, DValVal-DValValValVal-X
A47934staA1A-TA-THpGDHpGHpGHpGHpGHpGhttp://www.ncbi.nlm.nih.gov/pubmed/12060705"- staB E-domain is nonfunctional because of His-Pro mutation - CX in the end is either non-functional or L-selective"
2C-A-T-ECglyc-A-T-EDTyrTyrTyrTyrTyrTyrC-glyc linking hydroxyX
staB3C-A-T-ECglyc-A-T-E*-comDDHpGHpGDHpGDHpGDHpGDHpGC-glyc linking hydroxyX
staC4C-A-T-Ecom-Cglyc-A-T-ELHpGHpG2ClHpGHpGHpGHpGC-glyc linking hydroxyX
5C-A-T-ECglyc-A-T-EDHpGHpGHpGHpGHpGHpGC-glyc linking hydroxyX
6C-A-TCglyc-A-TDbhtTyrb-ObhtbhtbhtbhtC-glyc linking hydroxy
staD7C-A-T-E-TEcom-Cglyc-A-T-CX-TEL, LDHpGDHpGDHpGDHpGDHpGDHpGC-glyc linking hydroxy
ArthrofactinarfA1C-A-TC-A-TLeuLeuLeuLeuLeuLeuhttp://www.ncbi.nlm.nih.gov/pubmed/14522057Paper claims that there are epimerisation domains, but the dual domains sound more reasonable.
2C-A-TCDual-A-TAspAspAspAspAspAspX
arfB3C-A-TCDual-A-TThrThrThrThrThrThrX
4C-A-TCDual-A-TLeuLeuLeuLeuLeuLeuX
5C-A-TCDual-A-TLeuLeuLeuLeuLeuLeuX
6C-A-TCDual-A-TSerSerSerSerSerSerX
arfC7C-A-TCDual-A-TLeuLeuLeuLeuLeuLeuX
8C-A-TC-A-TLSerSerSerSerSerSer
9C-A-TCDual-A-TIleIleIleIleIleIleX
10C-A-TC-A-TLIleIleIleIleIleIle
11C-A-T-TE-TEC-A-T-TE-TEL,LAspAspAspAspAspAsp
BacitracinbacA1A-TA-TIleIleIleIleIleIlehttp://www.ncbi.nlm.nih.gov/pubmed/9427658
2C-A-TCy-A-TLCysCysCysCysCysCys
3C-A-TC-A-TLLeuLeuLeuLeuLeuLeu
4C-A-T-EC-A-T-ELGluGluGluGluGluD-Glu
5C-A-TC-A-TDIleIleIleIleIleIle
bacB6C-A-TC-A-TLLysLysLysLysLysLys
7C-A-T-EC-A-T-ELOrnOrnOrnOrnOrnD-Orn
bacC8C-A-Tcom-C-A-TDIleIleIleIleIleIle
9C-A-T-EC-A-T-ELPhePhePhePhePheD-Phe
10C-A-TC-A-TDHisHisTyrHisHisHis
11C-A-T-EC-A-T-ELAspAspAspAspAspD-Asp
12C-A-T-TEC-A-T-TED, LAsnAsnAsnAsnAsnAsn
CDAcdaPSI1C-A-TCSt-A-TSerSerSerSerSerSerhttp://www.ncbi.nlm.nih.gov/pubmed/12445768Not sure why Cglyc instead of C since there is no modification here.
2C-A-TC-A-TLThrThrThrThrThrThr
3C-A-EC-A-T-ELTrpTrpTrpTrpTrpTrpX
4C-A-TC-A-TDAspAspAspAspAspAsp
5C-A-TC-A-TLAspAspAspAspAspAsp
6C-A-EC-A-T-ELHpGHpGHpGHpGHpGHpGX
cdaPS27C-A-TCglyc-A-TDAspAspAspAspAspAspno glycosylation here
8C-A-TC-A-TLGlyGlyGlyGlyGlyGly
9C-A-EC-A-T-ELAsnAsnAsnAsnAsnAsnX
cdaPS310C-A-Tcom-C-A-TDGlu/Glu3MeGluMe3Asp/AsnGluAsnGluMe3
11C-A-T-TEC-A-T-TEL, LTrpTrpTrpTrpTrpTrp
CyclosporinsimA1C-A-TC-A-T???D-AlaD-AlaProD-AlaAlaD-Ala"http://www.ncbi.nlm.nih.gov/pubmed/8376400
domain order: http://www.ncbi.nlm.nih.gov/pubmed/16895337
D-Ala:http://www.ncbi.nlm.nih.gov/pubmed/8175682"
final C-domain is never metioned anywhere, but since the product is cyclic it might have similar function as a thioesterase. Thus it is uncertain, how the stereochemistry of the first alanine is achieved.
2C-A-TC-A-NM-TLLeuLeuval,leu,ile,abu,ivaLeuLeuLeuN-Methylierung
3C-A-TC-A-NM-TLLeuLeuval,leu,ile,abu,ivaLeuLeuLeuN-Methylierung
4C-A-TC-A-NM-TLValValval,leu,ile,abu,ivaValValValN-Methylierung
5C-A-TC-A-NM-TLBmtBmtphe,trp,phg,tyr,bhtBmtBmtBmtN-Methylierung
6C-A-TC-A-TLAbuAbuval,leu,ile,abu,ivaAbuAbu
7C-A-TC-A-NM-TLGly (NM > Sar)GluProGlySarsarcosineN-Methylierung
8C-A-TC-A-NM-TLLeuLeuval,leu,ile,abu,ivaLeuLeuLeuN-Methylierung
9C-A-TC-A-TLValValProValValVal
10C-A-TC-A-NM-TLLeuLeuval,leu,ile,abu,ivaLeuLeuLeuN-Methylierung
11C-A-TC-A-TLAlaAlaProAlaAlaAla
12CC???
Gramicidingramicidin synthetase 11A-T-EA-T-EDPheD-PhePhePhePhePheXhttp://www.ncbi.nlm.nih.gov/pubmed/1560782"On the genomic sequence for first synthetase are an additional TE and an additional Com-C domain on separate gene products. Two primary peptides can be fused to one ring."
grsB2C-A-Tcom-C-A-TLProProProProProPro
3C-A-TC-A-TLValValValValValVal
4C-A-TC-A-TLOrnOrnOrnOrnOrnOrn
5C-A-T-TEC-A-T-TEL, LLeuLeuLeuLeuLeuLeu
LichenycinlicA1C-A-TCSt-A-TGlnGlnGlnGlnGlnGlnhttp://www.ncbi.nlm.nih.gov/pubmed/9864322Separate TE domain has unknown function and can't be predicted. The first C-Domain and the Thioesterase put a beta-hydroxy fatty acid in the circular peptide
2C-A-TC-A-TLLeuLeuLeuLeuLeuLeu
3C-A-T-EC-A-T-ELLeuD-LeuLeuLeuLeuLeuX
licB4C-A-Tcom-C-A-TDValValValValValVal
5C-A-TC-A-TLAspAspAspAspAspAsp
6C-A-T-EC-A-T-ELLeuD-LeuLeuLeuLeuLeuX
licC7C-A-T-TEcom-C-A-T-TED, LIleIleIleIleIleIle/Val/Leu
licTE (deleted)TETE
SyringomycinsyrE1C-A-TCst-A-TSerSerSerSerSerSerhttp://www.ncbi.nlm.nih.gov/pubmed/9830033syrB1 is 9th module somehow attaching to C-TE after 8th module.
2C-A-TCdual-A-TLSerD-SerSerSerSerSerX
3C-A-TCdual-A-TDDabD-Dabgly,ala,val,leu,ile,abu,ivaDabDabDabX
4C-A-TCdual-A-TDDabDabgly,ala,val,leu,ile,abu,ivaDabDabDabX
5C-A-TC-A-TLArgArgArgArgArgArg
6C-A-TC-A-TLPhePhePhePhePhePhe
7 (not curated)C-A-TC-A-TLDhBu-3OHThrThrThrmaybe Thr is recognised and Cdual is dehydrating instead of racemising
8C-A-TCdual-A-TXAspAsp-3OHAspAspAlaAspX
C-T-TEC-T-TEL, Lonly TE kept
syrB1 (del)9A-TA-TThrThr-4ClThr