Team:Heidelberg/Templates/NRPS-W-23

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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.

Pathway	Gene	Module	SBSPKS domains	HMM domains	Specificity (Chirality C, TE)	Specificity (CA Substrate)	SBSPKS	SVM (0)	Stachelhaus (0)	Minowa (1)	Literature	Modifications	E-domain contained	Literature references	Comment
Actinomycin	acmA	1	A	A	-	4-MHA	4-MHA	hydrophobic/alphatic	PIP	4-MHA	4-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"
	acmB	2	C-A-T	CSt-A-T	-/4-MHA	Thr	Thr	Thr	Thr	Thr	Thr	-
		3	C-A-T-E	C-A-T-E-com	L	Val	D-Val	Val	Val	Val	Val	-	X
	acmC	4	C-A-T	com-C-A-T	D	Pro	Pro	Pro	Pro	Pro	Pro	-
		5	C-A-M-T	C-A-NM-T	L	Gly	Gly	Gly	Gly	Gly	Gly	N-Methylierung
		6	C-A-M-T-TE	C-A-NM-T-TE	L, L	Val	Val	Val	Val	Val	Val	N-Methylierung
ACV	acvA	1	A-T	A-T	-	Aad	Aad	Aad	Aad	Aad	Aad	-		"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 "
		2	C-A-T	C-A-T	D (pred) / L (sbspks, lit)	Cys	Cys	Cys	Cys	Cys	Cys	-
		3	C-A-T-E-TE	C-A-T-E-TE	L, D	Val	Val-D	Val	Val	Val	Val	-	X
A47934	staA	1	A-T	A-T		HpG	DHpG	HpG	HpG	HpG	HpG			http://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"
		2	C-A-T-E	Cglyc-A-T-E	D	Tyr	Tyr	Tyr	Tyr	Tyr	Tyr	C-glyc linking hydroxy	X
	staB	3	C-A-T-E	Cglyc-A-T-E*-com	D	DHpG	HpG	DHpG	DHpG	DHpG	DHpG	C-glyc linking hydroxy	X
	staC	4	C-A-T-E	com-Cglyc-A-T-E	L	HpG	HpG2Cl	HpG	HpG	HpG	HpG	C-glyc linking hydroxy	X
		5	C-A-T-E	Cglyc-A-T-E	D	HpG	HpG	HpG	HpG	HpG	HpG	C-glyc linking hydroxy	X
		6	C-A-T	Cglyc-A-T	D	bht	Tyrb-O	bht	bht	bht	bht	C-glyc linking hydroxy
	staD	7	C-A-T-E-TE	com-Cglyc-A-T-CX-TE	L, L	DHpG	DHpG	DHpG	DHpG	DHpG	DHpG	C-glyc linking hydroxy
Arthrofactin	arfA	1	C-A-T	C-A-T		Leu	Leu	Leu	Leu	Leu	Leu			http://www.ncbi.nlm.nih.gov/pubmed/14522057	Paper claims that there are epimerisation domains, but the dual domains sound more reasonable.
		2	C-A-T	CDual-A-T		Asp	Asp	Asp	Asp	Asp	Asp		X
	arfB	3	C-A-T	CDual-A-T		Thr	Thr	Thr	Thr	Thr	Thr		X
		4	C-A-T	CDual-A-T		Leu	Leu	Leu	Leu	Leu	Leu		X
		5	C-A-T	CDual-A-T		Leu	Leu	Leu	Leu	Leu	Leu		X
		6	C-A-T	CDual-A-T		Ser	Ser	Ser	Ser	Ser	Ser		X
	arfC	7	C-A-T	CDual-A-T		Leu	Leu	Leu	Leu	Leu	Leu		X
		8	C-A-T	C-A-T	L	Ser	Ser	Ser	Ser	Ser	Ser
		9	C-A-T	CDual-A-T		Ile	Ile	Ile	Ile	Ile	Ile		X
		10	C-A-T	C-A-T	L	Ile	Ile	Ile	Ile	Ile	Ile
		11	C-A-T-TE-TE	C-A-T-TE-TE	L,L	Asp	Asp	Asp	Asp	Asp	Asp
Bacitracin	bacA	1	A-T	A-T		Ile	Ile	Ile	Ile	Ile	Ile			http://www.ncbi.nlm.nih.gov/pubmed/9427658
		2	C-A-T	Cy-A-T	L	Cys	Cys	Cys	Cys	Cys	Cys
		3	C-A-T	C-A-T	L	Leu	Leu	Leu	Leu	Leu	Leu
		4	C-A-T-E	C-A-T-E	L	Glu	Glu	Glu	Glu	Glu	D-Glu
		5	C-A-T	C-A-T	D	Ile	Ile	Ile	Ile	Ile	Ile
	bacB	6	C-A-T	C-A-T	L	Lys	Lys	Lys	Lys	Lys	Lys
		7	C-A-T-E	C-A-T-E	L	Orn	Orn	Orn	Orn	Orn	D-Orn
	bacC	8	C-A-T	com-C-A-T	D	Ile	Ile	Ile	Ile	Ile	Ile
		9	C-A-T-E	C-A-T-E	L	Phe	Phe	Phe	Phe	Phe	D-Phe
		10	C-A-T	C-A-T	D	His	His	Tyr	His	His	His
		11	C-A-T-E	C-A-T-E	L	Asp	Asp	Asp	Asp	Asp	D-Asp
		12	C-A-T-TE	C-A-T-TE	D, L	Asn	Asn	Asn	Asn	Asn	Asn
CDA	cdaPSI	1	C-A-T	CSt-A-T		Ser	Ser	Ser	Ser	Ser	Ser			http://www.ncbi.nlm.nih.gov/pubmed/12445768	Not sure why Cglyc instead of C since there is no modification here.
		2	C-A-T	C-A-T	L	Thr	Thr	Thr	Thr	Thr	Thr
		3	C-A-E	C-A-T-E	L	Trp	Trp	Trp	Trp	Trp	Trp		X
		4	C-A-T	C-A-T	D	Asp	Asp	Asp	Asp	Asp	Asp
		5	C-A-T	C-A-T	L	Asp	Asp	Asp	Asp	Asp	Asp
		6	C-A-E	C-A-T-E	L	HpG	HpG	HpG	HpG	HpG	HpG		X
	cdaPS2	7	C-A-T	Cglyc-A-T	D	Asp	Asp	Asp	Asp	Asp	Asp	no glycosylation here
		8	C-A-T	C-A-T	L	Gly	Gly	Gly	Gly	Gly	Gly
		9	C-A-E	C-A-T-E	L	Asn	Asn	Asn	Asn	Asn	Asn		X
	cdaPS3	10	C-A-T	com-C-A-T	D	Glu/Glu3Me	GluMe3	Asp/Asn	Glu	Asn	GluMe3
		11	C-A-T-TE	C-A-T-TE	L, L	Trp	Trp	Trp	Trp	Trp	Trp
Cyclosporin	simA	1	C-A-T	C-A-T	???	D-Ala	D-Ala	Pro	D-Ala	Ala	D-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.
		2	C-A-T	C-A-NM-T	L	Leu	Leu	val,leu,ile,abu,iva	Leu	Leu	Leu	N-Methylierung
		3	C-A-T	C-A-NM-T	L	Leu	Leu	val,leu,ile,abu,iva	Leu	Leu	Leu	N-Methylierung
		4	C-A-T	C-A-NM-T	L	Val	Val	val,leu,ile,abu,iva	Val	Val	Val	N-Methylierung
		5	C-A-T	C-A-NM-T	L	Bmt	Bmt	phe,trp,phg,tyr,bht	Bmt	Bmt	Bmt	N-Methylierung
		6	C-A-T	C-A-T	L	Abu	Abu	val,leu,ile,abu,iva	Abu	Abu
		7	C-A-T	C-A-NM-T	L	Gly (NM > Sar)	Glu	Pro	Gly	Sar	sarcosine	N-Methylierung
		8	C-A-T	C-A-NM-T	L	Leu	Leu	val,leu,ile,abu,iva	Leu	Leu	Leu	N-Methylierung
		9	C-A-T	C-A-T	L	Val	Val	Pro	Val	Val	Val
		10	C-A-T	C-A-NM-T	L	Leu	Leu	val,leu,ile,abu,iva	Leu	Leu	Leu	N-Methylierung
		11	C-A-T	C-A-T	L	Ala	Ala	Pro	Ala	Ala	Ala
		12	C	C	???
Gramicidin	gramicidin synthetase 1	1	A-T-E	A-T-E	D	Phe	D-Phe	Phe	Phe	Phe	Phe		X	http://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."
	grsB	2	C-A-T	com-C-A-T	L	Pro	Pro	Pro	Pro	Pro	Pro
		3	C-A-T	C-A-T	L	Val	Val	Val	Val	Val	Val
		4	C-A-T	C-A-T	L	Orn	Orn	Orn	Orn	Orn	Orn
		5	C-A-T-TE	C-A-T-TE	L, L	Leu	Leu	Leu	Leu	Leu	Leu
Lichenycin	licA	1	C-A-T	CSt-A-T		Gln	Gln	Gln	Gln	Gln	Gln			http://www.ncbi.nlm.nih.gov/pubmed/9864322	Separate 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
		2	C-A-T	C-A-T	L	Leu	Leu	Leu	Leu	Leu	Leu
		3	C-A-T-E	C-A-T-E	L	Leu	D-Leu	Leu	Leu	Leu	Leu		X
	licB	4	C-A-T	com-C-A-T	D	Val	Val	Val	Val	Val	Val
		5	C-A-T	C-A-T	L	Asp	Asp	Asp	Asp	Asp	Asp
		6	C-A-T-E	C-A-T-E	L	Leu	D-Leu	Leu	Leu	Leu	Leu		X
	licC	7	C-A-T-TE	com-C-A-T-TE	D, L	Ile	Ile	Ile	Ile	Ile	Ile/Val/Leu
	licTE (deleted)	TE	TE
Syringomycin	syrE	1	C-A-T	Cst-A-T		Ser	Ser	Ser	Ser	Ser	Ser			http://www.ncbi.nlm.nih.gov/pubmed/9830033	syrB1 is 9th module somehow attaching to C-TE after 8th module.
		2	C-A-T	Cdual-A-T	L	Ser	D-Ser	Ser	Ser	Ser	Ser		X
		3	C-A-T	Cdual-A-T	D	Dab	D-Dab	gly,ala,val,leu,ile,abu,iva	Dab	Dab	Dab		X
		4	C-A-T	Cdual-A-T	D	Dab	Dab	gly,ala,val,leu,ile,abu,iva	Dab	Dab	Dab		X
		5	C-A-T	C-A-T	L	Arg	Arg	Arg	Arg	Arg	Arg
		6	C-A-T	C-A-T	L	Phe	Phe	Phe	Phe	Phe	Phe
		7 (not curated)	C-A-T	C-A-T	L		DhBu-3OH	Thr	Thr	Thr		maybe Thr is recognised and Cdual is dehydrating instead of racemising
		8	C-A-T	Cdual-A-T	X	Asp	Asp-3OH	Asp	Asp	Ala	Asp		X
			C-T-TE	C-T-TE	L, L	only TE kept
	syrB1 (del)	9	A-T	A-T		Thr	Thr-4Cl				Thr

Revision as of 03:20, 29 October 2013 (view source) JuliaS1992 (Talk \| contribs) (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 ...") ← Older edit		Latest revision as of 03:21, 29 October 2013 (view source) JuliaS1992 (Talk \| contribs)
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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.