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Model Overview

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1471

Sequence

UniProt

P32492

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING

P32492: 4932.YAL029C

Domain

Link to: [ InterPro ]

	Myosin_head
	IQ
	DIL

Model 3D Structure

	Model information:
	Modelled residue range:	1103 to 1444
	Based on template:	[ 3mmi ]
	Sequence Identity [%]:	95%
	Model date:	2013-02-18
	Revision date:	2013-01-30

Quaternary structure information:	[details]
Template (3mmi): MONOMER Model: MONOMER

Ligand information:	[details]
Ligands in the template: none. Ligands in the model: none.

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

This model has not been updated since 2013-01-30. 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    1       DLLELLMD LNCYTLEVTE GYLKKVNVTE VNGDNVLGPI HVITTVVSSL
3mmi_1#1  1103    dllellmd lncytlevte gylkkvnvte vng---lgpi hvittvvssl
                                                                      
TARGET             hhhhh    hhhhhhhh                     hh hhhhhhhhhh
3mmi_1#1           hhhhh    hhhhhhhh                     hh hhhhhhhhhh


TARGET    49    VRNGLLIQSS KFISKVLLTV ESIVMSLPKD ETMLGGIFWL SNLSRLPAFA
3mmi_1#1  1151  vrnglliqss kfiskvlltv esivmslpkd etmlggifwl snlsrlpafa
                                                                      
TARGET          h   hhhhhh hhhhhhhhhh hhhhhh      hhhhhhhhh hhhhhhhhhh
3mmi_1#1        h   hhhhhh hhhhhhhhhh hhhhhh      hhhhhhhhh hhhhhhhhhh


TARGET    99    ANQKTLYEAN GGDEKDKLTL IYLNDLENET LKVFDKIYST WLVKFMKHAS
3mmi_1#1  1201  anqktly--- -----dkltl iylndlenet lkvfdkiyst wlvkfmkhas
                                                                      
TARGET          hhhh              hhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh
3mmi_1#1        hhhhh            hhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh


TARGET    149   AHIEIFDMVL NEKLFKNSGD EKFAKLFTFL NEFDAVLCKF QVVDSMHTKI
3mmi_1#1  1251  ahieifdmvl neklfknsgd ekfaklftfl nefdavlckf qvvdsmhtki
                                                                      
TARGET          hh   hhh            h hhhhhhhhhh hhhhhhhhh     hhhhhhh
3mmi_1#1        hh   hhh            h hhhhhhhhhh hhhhhhhhh     hhhhhhh


TARGET    199   FNDTLKYLNV MLFNDLITKC PALNWKYGYE VDRNIERLVS WFEPRIEDVR
3mmi_1#1  1301  fndtlkylnv mlfndlitkc palnwkygye vdrnierlvs wfepriedvr
                                                                      
TARGET          hhhhhhhhhh hhhhhhhh       hhhhhh hhhhhhhhhh hh       h
3mmi_1#1        hhhhhhhhhh hhhhhhhh       hhhhhh hhhhhhhhhh hh       h


TARGET    249   PNLIQIIQAV KILQLKISNL NEFKLLFDFW YALNPAQIQA ILLKYKPANK
3mmi_1#1  1351  pnliqiiqav kilqlkisnl nefkllfdfw yalnpaqiqa illkykp---
                                                                      
TARGET          h   hhhhhh hhhh     h hhhhhh         hhhhhh hhh       
3mmi_1#1        h   hhhhhh hhhh     h hhhhhh         hhhhhh hhh       


TARGET    299   GEAGVPNEIL NYLANVIKRE NLSLPGKMEI MLSAQFDSAK NHLR      
3mmi_1#1  1398  --agvpneil nylanvikre nlslpgkmei mlsaqfdsak nhlr-     
                                                                      
TARGET                hhhh hhhhhhhhhh hhh                             
3mmi_1#1              hhhh hhhhhhhhhh hhh

Quality

[ start new quality assessment in Workspace ]

Ligand Modelling Log

Template's ligands section 
Template without ligands. 
No ligands were included in the model.

Oligomer Modelling Log

Quaternary Structure Annotation of the Template 
 3mmi is annotated as MONOMER 
 The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry 
 The following biological unit was used to build the template structure: 3mmi.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template can be assumed to be similar (=MONOMER) 
 The corresponding reliability score is 0.818 (>0.5 indicates similarity) 
 Model was succesfully built as MONOMER.

Template Selection

 - Start SMR-Pipeline for:592fd5f0eb506e8e01c36e67d3f5345c on BC2-cluster at Mon Feb 18 12:16:34
2013 


 - 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...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with B found
 - No template with C found
 - No template with Y found
 - No template with Z found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with Y found
 - No template with Z found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with Y found
 - No template with Z found
 - No template with Y found
 - No template with Z found
 - No template with B found
 - No template with B found
 - No template with F found
 - No template with B found
 - No template with H found
 - No template with D found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with F found
 - No template with B found
 - No template with H found
 - No template with D found
 - No template with B found
 - No template with D found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with Y found
 - No template with Z found
 - No template with B found
 - No template with B found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:3): model based on new templates
 - Send 3 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                             *******************
 - building model based on 3mmiA (1103-1444) was successful 
 - ******************************************
 - building model based on 1w8jA (8-778) was successful 
 - **********************************************
 - building model based on 2bkiA (4-840) was successful 
 - Repository Pipeline parameter

   Cut-off parameters to model the target based on a BLAST target-template alignment
    Evalue :                                     0.0001
    Minimum Template size (aa) for ranking :     25
    Minimum Sequence identity :                  60

   Cut-off parameters to model the target based on a HHSearch target-template alignment
    Evalue :                                     0.0001
    Probability :                                50
    MAC :                                        0.3

   Parameters for model selection
    Minimal number of uncovered target
     residues after BLAST to run HHSEARCH :      50
    Minimal number of uncovered target
     residues to model an additional template :  25
    
 - Finish SMR-Pipeline for:592fd5f0eb506e8e01c36e67d3f5345c on BC2-cluster at Mon Feb 18 12:31:30
2013

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

3mmi: CRYSTAL STRUCTURE OF THE GLOBULAR TAIL OF MYO4P
Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	1103-1444	3mmiA	95%	>target DLLELLMDLNCYTLEVTEGYLKKVNVTEVNGDNVLGPIHVITTVVSSLVRNGLLIQSSKFISKVLLTVESIVMSLPKDETMLGGIFWLSNLSRLPAFAANQKTLYEANGGDEKDKLTLIYLNDLENETLKVFDKIYSTWLVKFMKHASAHIEIFDMVLNEKLFKNSGDEKFAKLFTFLNEFDAVLCKFQVVDSMHTKIFNDTLKYLNVMLFNDLITKCPALNWKYGYEVDRNIERLVSWFEPRIEDVRPNLIQIIQAVKILQLKISNLNEFKLLFDFWYALNPAQIQAILLKYKPANKGEAGVPNEILNYLANVIKRENLSLPGKMEIMLSAQFDSAKNHLR >3mmiA DLLELLMDLNCYTLEVTEGYLKKVNVTEVNG---LGPIHVITTVVSSLVRNGLLIQSSKFISKVLLTVESIVMSLPKDETMLGGIFWLSNLSRLPAFAANQKTLY--------DKLTLIYLNDLENETLKVFDKIYSTWLVKFMKHASAHIEIFDMVLNEKLFKNSGDEKFAKLFTFLNEFDAVLCKFQVVDSMHTKIFNDTLKYLNVMLFNDLITKCPALNWKYGYEVDRNIERLVSWFEPRIEDVRPNLIQIIQAVKILQLKISNLNEFKLLFDFWYALNPAQIQAILLKYKP-----AGVPNEILNYLANVIKRENLSLPGKMEIMLSAQFDSAKNHLR [Model]
	1101-1468	3mmiB	94%	>target NPDLLELLMDLNCYTLEVTEGYLKKVNVTEVNGDNVLGPIHVITTVVSSLVRNGLLIQSSKFISKVLLTVESIVMSLPKDETMLGGIFWLSNLSRLPAFAANQKTLYEANGGDEKDKLTLIYLNDLENETLKVFDKIYSTWLVKFMKHASAHIEIFDMVLNEKLFKNSGDEKFAKLFTFLNEFDAVLCKFQVVDSMHTKIFNDTLKYLNVMLFNDLITKCPALNWKYGYEVDRNIERLVSWFEPRIEDVRPNLIQIIQAVKILQLKISNLNEFKLLFDFWYALNPAQIQAILLKYKPANKGEAGVPNEILNYLANVIKRENLSLPGKMEIMLSAQFDSAKNHLRYDTSAITQNSNTEGLATVSKIIKL >3mmiB NPDLLELLMDLNCYTLEVTEGYLKKVNVTEVNGDNVLGPIHVITTVVSSLVRNGLLIQSSKFISKVLLTVESIVMSLPKDETMLGGIFWLSNLSRLPAFAANQKTLY-------KDKLTLIYLNDLENETLKVFDKIYSTWLVKFMKHASAHIEIFDMVLNEKLFKNSGDEKFAKLFTFLNEFDAVLCKFQVVDSMHTKIFNDTLKYLNVMLFNDLITKCPALNWKYGYEVDRNIERLVSWFEPRIEDVRPNLIQIIQAVKILQLKISNLNEFKLLFDFWYALNPAQIQAILLKYKPAN---AGVPNEILNYLANVIKRENLSLPGKMEIMLSAQFDSAKNHLRY------------GLATVSKIIKL [Model]

4e7z: MYOSIN VI (MD) PRE-POWERSTROKE STATE, P21 CRYSTAL FORM
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

7-795

4e7zB

32%

>targetTKCWYPHKEQGWIGGEVTKNDFFEGTFHLELKLEDGETVSIETNSFENDDDHPTLPVLRNPPILESTDDLTTLSYLNEPAVLHAIKKRYMNGQIYTYSGIVLIAANPFDKVDHLYSREMIQNYSSKRKDELEPHLFAIAEEAYRFMVHEKANQTVVVSGESGAGKTVSAKYIMRYFASVQESNNREGEVEMSQIESQILATNPIMEAFGNAKTTRNDNSSRFGKYLQILFDENTTIRGSKIRTYLLEKSRLVYQPETERNYHIFYQILEGLPEPVKQELHLSSPKDYHYTNQG--------------------------GQPNIAGIDEAREYKITTDALSLVGINHETQLGIFKILAGLLHIGNIEMKMTRNDASLSSEEQNLQIACELLGIDPFNFAKWIVKKQIVTRSEKIVTNLNYNQALIARDSVAKFIYSTLFDWLVDNINKTLYDPELDQQDHVFSFIGILDIYGFEHFEKNSFEQFCINYANEKLQQEFNQHVFKLEQEEYVKEEIEWSFIEFSDNQPCIDLIENK-LGILSLLDEESRLPSGSDESWASKLYSAFNKPPSNEVFSKPRF----------GQTKFIVSHYAVDVEYEVEGFIEKNRDSVSLGHLDVFKATTNPIFKQILDNRELRSDDAPEEQNTEKKIMIPARLSQKKPTLGSMFKKSLGELMAIINSTNVHYIRCIKPNSEKKPWEFDNLMVLSQLRACGVLETIRISCAGFPSRWTFDEFVQRYFLLTDYSLWSGILYNPDLPKEAIVNFCQSILDATISDSAKYQIGNTKIFFKAGMLAFLEKLRTNKMNEICIIIQKKIRARY>4e7zBKPVWAPHPTDGFQVGNIVDIGPDS--LTIEPLNQKGKTFLALINQVFPA----------EEDSKKDVEDNCSLMYLNEATLLHNIKVRYSKDRIYTYVANILIAVNPYFDIPKIYSSETIKSYQGKSLGTMPPHVFAIADKAFRDMKVLKLSQSIIVSGESGAGKTENTKFVLRYLTESYGTGQ--------DIDDRIVEANPLLEAFGNAKTVRNNNSSRFGKFVEIHFNEKSSVVGGFVSHYLLEKSRICVQGKEERNYHIFYRLCAGASEDIRERLHLSSPDNFRYLNRGCTRYFANKETDKQILQNRKSPEYLKAGSLKDPLLDDHGDFIRMCTAMKKIGLDDEEKLDLFRVVAGVLHLGNIDFEEGCN--LKNKSTQALEYCAELLGLDQDDLRVSLTTRVV---------PLKVEQANNARDALAKTVYSHLFDHVVNRVNQCFPFET------SSYFIGVLDIAGFEYFEHNSFEQFCINYCNEKLQQFFNERILKEEQELYQKEGLGVNEVHYVDNQDCIDLIEARLVGILDILDEENRLPQPSDQHFTSAVHQKHKDHFR---LSIPRKSKLAIHRNIRDDEGFIIRHFAGAVCYETTQFVEKNNDALHMSLESLICESRDKFIRELFEL--------------------------SFISVGNKFKTQLNLLLDKLRSTGASFIRCIKPNLKMTSHHFEGAQILSQLQCSGMVSVLDLMQGGFPSRASFHELYNMYKKYLARL--------------DPRLFCKALFKALGLNEIDYKFGLTKVFFRPGKFAEFDQIMKSDPDHLAELKR--VNHWL

[Model]

4anj: MYOSIN VI (MDINSERT2-GFP FUSION) PRE-POWERSTROKE STATE (MG
Solved by: X-RAY, Resolution: 2.60A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

6-820

4anjA

31%

>targetGTKCWYPHKEQGWIGGEVTKNDFFEGTFHLELKLEDGETVSIETNSFENDDDHPTLPVLRNPPILESTDDLTTLSYLNEPAVLHAIKKRYMNGQIYTYSGIVLIAANPFDKVDHLYSREMIQNYSSKRKDELEPHLFAIAEEAYRFMVHEKANQTVVVSGESGAGKTVSAKYIMRYFASVQESNNREGEVEMSQIESQILATNPIMEAFGNAKTTRNDNSSRFGKYLQILFDENTTIRGSKIRTYLLEKSRLVYQPETERNYHIFYQILEGLPEPVKQELHLSSPKDYHYTNQGG--------------------------QPNIAGIDEAREYKITTDALSLVGINHETQLGIFKILAGLLHIGNIEMKMTRNDASLSSEEQNLQIACELLGIDPFNFAKWIVKKQIVTRSEKIVTNLNYNQALIARDSVAKFIYSTLFDWLVDNINKTLYDPELDQQDHVFSFIGILDIYGFEHFEKNSFEQFCINYANEKLQQEFNQHVFKLEQEEYVKEEIEWSFIEFSDNQPCIDLIENKL-GILSLLDEESRLPSGSDESWASKLYSAFNKPPSNEVFSKPR-------FGQTKFIVSHYAVDVEYEVEGFIEKNRDSVSLGHLDVFKATTNPIFKQILDNRELRSDDAPEEQNTEKKIMIPARLSQKKPTLGSMFKKSLGELMAIINSTNVHYIRCIKPNSEKKPWEFDNLMVLSQLRACGVLETIRISCAGFPSRWTFDEFVQRYFLLTDYSLWSGILYNPDLPKEAIVNFCQSILDATISDSAKYQIGNTKIFFKAGMLAFLEKLRTNKMNEICIIIQKKIRARYYRLQYLQTMESIKKCQSQIRSLLVR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------>4anjAGKPVWAPHPTDGFQVGNIVDIGPDS--LT--IEPLKT--FLALINQVFP----------AEEDSKKDVEDNCSLMYLNEATLLHNIKVRYSKDRIYTYVANILIAVNPYFDIPKIYSSETIKSYQGKSLGTMPPHVFAIADKAFRDMKVLKLSQSIIVSGESGAGKTENTKFVLRYLTESYG-----------TIDDRIVEANPLLEAFGNAKTVRNNNSSRFGKFVEIHFNEKSSVVGGFVSHYLLEKSRICVQGKEERNYHIFYRLCAGASEDIRERLHLSSPDNFRYLNRGCTRYFANKETDKQILQNRKSPEYLKAGSLKDPLLDDHGDFIRMCTAMKKIGLDDEEKLDLFRVVAGVLHLGNIDFEECNLK---NKSTQALEYCAELLGLDQDDLRVSLTTR--------VKVPLKVEQANNARDALAKTVYSHLFDHVVNRVNQCFPFET------SSYFIGVLDIAGFEYFEHNSFEQFCINYCNEKLQQFFNERILKEEQELYQKEGLGVNEVHYVDNQDCIDLIEARLVGILDILDEENRLPQPSDQHFTSAVHQKHKDHFRLSIPRKSKLAIHRNIRDDEGFIIRHFAGAVCYETTQFVEKNNDALHMSLESLICESRDKFIRELFE---------------------------SFISVGNKFKTQLNLLLDKLRSTGASFIRCIKPNLKMTSHHFEGAQILSQLQCSGMVSVLDLMQGGFPSRASFHELYNMYKKYMPDKLA----------RLDPRLFCKALFKALGLNEIDYKFGLTKVFFRPGKFAEFDQIMKSDPDHLAELV-KRVNHWLICSRWKKVQWCSLSVIKLKNKIKYRAEAVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFVQCFARYPDHMRQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLLEFVTAAG

[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.