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Model Overview

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939

Sequence

UniProt

P19809

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING

P19809: 574521.E2348C_39

Domain

Link to: [ InterPro ]

	LysM
	Big_2
	Big_1
	Big_1
	Intimin_C
	DUF3442

Model 3D Structure

	Model information:
	Modelled residue range:	61 to 115
	Based on template:	[ 1e0g ]
	Sequence Identity [%]:	16%
	Model date:	2009-12-21
	Revision date:	2009-12-21

Quaternary structure information:	[details]
NA

Ligand information:	[details]
NA

Template Links: [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2009-12-21. In the meantime, new template structures may have become available which would allow building a more reliable model. Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now? [ Submit ]

Alignment


TARGET    61      NRLFYTLK TGETVADLSK SQDINLSTIW SLNKHLYSSE SEMMKAAPGQ
1e0gA     1       dsityrvr kgdslssiak rhgvnikdvm rwns-dt--- -a--nlqpgd
                                                                      
TARGET              sssss      hhhhhh       hhhh hh         hhhh     s
1e0gA               sssss      hhhhhh      hhhhh hh                  s


TARGET    109   QIILPLK                                               
1e0gA     42    kltlfvk-                                              
                                                                      
TARGET          ssss                                                  
1e0gA           ssss

Quality

[ start new quality assessment in Workspace ]

Ligand Modelling Log

no data available!

Oligomer Modelling Log

no data available!

Template Selection

 - Start SMR-Pipeline for:5073cc9bf4a3f67f9a5316402ee6f97a on BC2-cluster at Mon Dec 21 17:14:24
2009 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Run HHSearch to detect more templates...
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old5 vs new:4): model based on new templates
 - Send 4 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                         ************************
 - 1f00I (658-939) is a 100% match
 -                                                 ****************
 - building model based on 1cwvA (566-750) was successfull 
 -      *****
 - building model based on 1e0gA (61-115) was successfull 
 -                                        *****************************************
 - building model based on 1cwvA (454-938) was successfull 
 - Parameter file for Repository Pipeline
	
   BLAST
    Evalue :                              0.0001
    Minimum Template size for ranking :   25
    Minimum Sequence identity :           60
	
   HHSEARCH
    Evalue :                              0.0001
    Pvalue :                              50
    mact parameter:                       0.3
	
   RANKING
    Minimal number of uncovered target residues to go for HHSEARCH :           50
    Minimal number of uncovered target residues to accept additional model :   25
	
 - Finish SMR-Pipeline for:5073cc9bf4a3f67f9a5316402ee6f97a on BC2-cluster at Mon Dec 21 17:14:24
2009

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

1e5u:
Not available
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

753-939

1e5uI

100%

1f02:
Not available
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

658-939

1f02I

100%

[Model]

2zqk:
Not available
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

750-939

2zqkA

48%

1f00:
Not available
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

658-939	1f00I	100%	>target ASITEIKADKTTAVANGQDAITYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTLTIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKASGGNGKYTWRSANPAIASVDASSGQVTLKEKGTTTISVISSDNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSSQNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCVK >1f00I ASITEIKADKTTAVANGQDAITYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTLTIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKASGGNGKYTWRSANPAIASVDASSGQVTLKEKGTTTISVISSDNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSSQNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCVK [Model]
658-939	1f00I	100%	>target ASITEIKADKTTAVANGQDAITYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTLTIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKASGGNGKYTWRSANPAIASVDASSGQVTLKEKGTTTISVISSDNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSSQNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCVK >1f00I ASITEIKADKTTAVANGQDAITYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTLTIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKASGGNGKYTWRSANPAIASVDASSGQVTLKEKGTTTISVISSDNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSSQNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCVK [Model]
559-738	1f00I	25%	>target -GVTDFTADKTSAKADGTEAITYTATVKKNGVAQANVPVSFNIVSGTAVLSANSANTNGSGKATVTLKSDKPGQVVVSAKTAEMTSALNANAVIFVDQTKASITEIKADKTTAVANGQDAI----TYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDT-NGYAKVTLTSTTPGKSLVSARVSD--------------------------------------------------------------------------------------------------------------- >1f00I ASITEIKADKTTAVANGQDAITYTVKVMKGDKPVSNQEVTFTTTLG--KLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTL--TIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKASG---GNGKYTWRSANPA----IASVDASSGQVTL----KEKGTTTISVISSDNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSSQNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCVK [Model]

1e0g:
Not available
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

61-115

1e0gA

16%

1cwv:
Not available
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

454-938	1cwvA	16%	>target --LSLNIPHDINGTER-STQKIQLIVKSKYG--L--DRIVWDDS--ALRSQGGQIQHSGSQSAQDYQAILPAYVQGGSNVYKVTARAYDRNGNSSNNVLLTITVLSNGQVVDQVGVTDFTADKTSAKADGTEAITYTATVKK-NGVAQANVPVSFNIVSGTAVLSANSANTNGSGKATVTLKSDKPGQVVVSAKTAEMTSALNANAVIFVDQTK--ASITEIKADKTTAVANGQDAITYTVKVMK-GDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTLTIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKAS---GGNGKYTWRSANPAIASVDASSGQVTLKEKGTT--TISVISS--DNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSS--------QNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCV--- >1cwvA LTLTAAVIGDGAPANGKTAITVEFTVADFEGKPLAGQEVVITTNNGALPNKITEK----TDANGVARIALTNTTD---GVTVVTAEVEGQRQ----SVDTHFVK--GTI---AADKSTLAAVPTSIIADGLMASTITLELKDTYGDPQAGANVAFDTTLGNMG----VITDHNDGTYSAPLTSTTLGVATVTVKVDGAAFSVPSVTVNFTADPIPDAGRSSFTVSTPDILADGTMSSTLSFVPVDKNGHFISGMQGLSFTQNGVPVSISPITEQPDSYTATVVGNSVGDVTITPQVDTLILSTLQKKISLFPVPTLTGILVNGQNFATDKGFPKTIFKNATFQLQMDNDVANNTQYEWSSSFTPNVSVN-DQGQVTITYQTYSEVAVTAKSKKFPSYSVSYRFY-PNRWIYDGGRSLVSSLEASRQCQGSDMSAVLESSRATNGTRAPDGTLWGEWGSLTAYSS--DWQSGEYWVKKTSTD-----FETMNMDTGALQPG---PAYLAFPLCALSI [Model]
566-750	1cwvA	26%	>target -------DKTSAKADGTEAITYTATVKK-NGVAQANVPVSFNIVSGTAVLSANSANTNGSGKATVTLKSDKPGQVVVSAKTAEMTSALNANAVIFVDQTKASITEIKADKTTAVANGQDAITYTVKVMK-GDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEF------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >1cwvA LTLTAAVIGDGAPANGKTAITVEFTVADFEGKPLAGQEVVITTNNGA-LPNKITEKTDANGVARIALTNTTDGVTVVTAEVEGQRQSVD--THFVKGTIAADKSTLAAVPTSIIADGLMASTITLELKDTYGDPQAGANVAFDTTLGNM--GVITDHNDGTYSAPLTSTTLGVATVTVKVDGAAFSVPSVTVNFTADPIPDAGRSSFTVSTPDILADGTMSSTLSFVPVDKNGHFISGMQGLSFTQNGVPVSISPITEQPDSYTATVVGNSVGDVTITPQVDTLILSTLQKKISLFPVPTLTGILVNGQNFATDKGFPKTIFKNATFQLQMDNDVANNTQYEWSSSFTPNVSVNDQGQVTITYQTYSEVAVTAKSKKFPSYSVSYRFYPNRWIYDGGRSLVSSLEASRQCQGSDMSAVLESSRATNGTRAPDGTLWGEWGSLTAYSSDWQSGEYWVKKTSTDFETMNMDTGALQPGPAYLAFPLCALSI [Model]
460-736	1cwvA	15%	>target -----------------------------------------------------------------------------------------------------------HDINGTERSTQKIQLIVKSKYGL----DRIVWDDSALRSQGGQIQHSGSQSAQDYQAILPAYVQGGSNVYKVTARAYDRNGNSSNNVLLTITVLSNGQVVDQVGVTDFTADKTSAKADGTEAITYTATVKK-NGVAQANVPVSFNIVSGTAVLSANSANTNGSGKATVTLKSDKPGQVVVSAKTAEMTSALNANAVIFVDQTKASITEIKADKTTAVANGQDAI----TYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARV------------------------------------------------------------------------------------------------------------------ >1cwvA LTLTAAVIGDGAPANGKTAITVEFTVADFEGKPLAGQEVVITTNNGALPNKITEKTDANGVARIALTNTTDGVTVVTAEVEGQRQSVDTHFVKGTIAADKSTLAAVPTSIIADGLMASTITLELKDTYGDPQAGANVAFDTT-----LGNMGVITDHNDGTYSAPLTSTTLG---VATVTVKVDGAAFSV-PSVTVNFTADPI----PDAGRSSFTVSTPDILADGTMSSTLSFVPVDKNGHFISGMQGLSFTQNGVP--VSISPITEQPDSYTATVVGNSVGDVTITPQVDTLILSTLQKKISLFPV--PTLTGILVNGQNFATDKGFPKTIFKNATFQLQMDNDVANNTQYEWSSSFTP----NVSVNDQGQVTI--TYQTYSEVAVTAKSKKFPSYSVSYRFYPNRWIYDGGRSLVSSLEASRQCQGSDMSAVLESSRATNGTRAPDGTLWGEWGSLTAYSSDWQSGEYWVKKTSTDFETMNMDTGALQPGPAYLAFPLCALSI [Model]

Downloads

download model.tgz

Reference

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.