Citrus Sinensis ID: 028882

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200--
MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRFRSTVWWRNVKLTYVLLADTCLYL
cccEEEEEEEccEEEcccccccccHHHHHHHHHcccccccccEEEEEEccEEEEEEEEccEEEEEEEccccccccHHHHHHHHHHHHHHHccHHHHHHccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEc
ccEEEEEEEcccEEEEEEccccccHHHHHHHHHHHcccccccEEEEEcccEEEEEEEcccEEEEEEEccHcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
MAILFSLVARGSVVLAECSATATNASAIARQILdkipgnndshvsysqdryifhvkrtdgltvlcmaddtagrripfaFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEyysddpnadrINRIKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRFRSTVWWRNVKLTYVLLADTCLYL
MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELlvdktanmqgntfrfrkqarrfrstvwwrnvkltyvlladtclyl
MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRFRSTVWWRNVKLTYVLLADTCLYL
**ILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYY***********I***MSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRFRSTVWWRNVKLTYVLLADTCLY*
MAILFSLVARGSVVLAECSATATNASAIARQILD**********SYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEY**************GEMSQVRNVMIENIDKVLERGDRLELLVD***************ARRFRSTVWWRNVKLTYVLLADTCLYL
MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRFRSTVWWRNVKLTYVLLADTCLYL
MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRFRSTVWWRNVKLTYVLLADTCLYL
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRFRSTVWWRNVKLTYVLLADTCLYL
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query202 2.2.26 [Sep-21-2011]
Q9LFP1221 Vesicle-associated membra yes no 0.965 0.882 0.826 2e-95
O49377219 Vesicle-associated membra no no 0.935 0.863 0.835 3e-93
Q9SIQ9219 Vesicle-associated membra no no 0.935 0.863 0.820 5e-92
Q9FMR5221 Vesicle-associated membra no no 0.975 0.891 0.577 1e-68
Q86AQ7260 Vesicle-associated membra yes no 0.965 0.75 0.456 7e-48
Q9JHW5220 Vesicle-associated membra yes no 0.940 0.863 0.387 2e-36
P70280220 Vesicle-associated membra yes no 0.940 0.863 0.376 4e-36
P47192221 Vesicle-associated membra no no 0.930 0.850 0.392 7e-36
Q5ZL74220 Vesicle-associated membra yes no 0.940 0.863 0.382 1e-35
P51809220 Vesicle-associated membra yes no 0.940 0.863 0.382 1e-35
>sp|Q9LFP1|VA713_ARATH Vesicle-associated membrane protein 713 OS=Arabidopsis thaliana GN=VAMP713 PE=2 SV=1 Back     alignment and function desciption
 Score =  348 bits (892), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 162/196 (82%), Positives = 187/196 (95%), Gaps = 1/196 (0%)

Query: 1   MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNN-DSHVSYSQDRYIFHVKRTD 59
           MAI+F+LVARG+VVL+E SAT+TNAS+I++QIL+K+PGN+ DSH+SYSQDRYIFHVKRTD
Sbjct: 1   MAIIFALVARGTVVLSEFSATSTNASSISKQILEKLPGNDSDSHMSYSQDRYIFHVKRTD 60

Query: 60  GLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYS 119
           GLTVLCMAD+TAGR IPFAFL+DIHQRFVKTYGRA+ SAQAY MNDEFSRVLSQQME+YS
Sbjct: 61  GLTVLCMADETAGRNIPFAFLDDIHQRFVKTYGRAIHSAQAYSMNDEFSRVLSQQMEFYS 120

Query: 120 DDPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRF 179
           +DPNADR++RIKGEMSQVRNVMIENIDKVL+RG+RLELLVDKT NMQGNTFRFRKQARR+
Sbjct: 121 NDPNADRMSRIKGEMSQVRNVMIENIDKVLDRGERLELLVDKTENMQGNTFRFRKQARRY 180

Query: 180 RSTVWWRNVKLTYVLL 195
           R+ +WWRNVKLT  L+
Sbjct: 181 RTIMWWRNVKLTIALI 196
Involved in the targeting and/or fusion of transport vesicles to their target membrane.
Arabidopsis thaliana (taxid: 3702)
>sp|O49377|VA711_ARATH Vesicle-associated membrane protein 711 OS=Arabidopsis thaliana GN=VAMP711 PE=2 SV=2 Back     alignment and function description
>sp|Q9SIQ9|VA712_ARATH Vesicle-associated membrane protein 712 OS=Arabidopsis thaliana GN=VAMP712 PE=3 SV=1 Back     alignment and function description
>sp|Q9FMR5|VA714_ARATH Vesicle-associated membrane protein 714 OS=Arabidopsis thaliana GN=VAMP714 PE=2 SV=1 Back     alignment and function description
>sp|Q86AQ7|VAM7B_DICDI Vesicle-associated membrane protein 7B OS=Dictyostelium discoideum GN=vamp7B PE=3 SV=1 Back     alignment and function description
>sp|Q9JHW5|VAMP7_RAT Vesicle-associated membrane protein 7 OS=Rattus norvegicus GN=Vamp7 PE=1 SV=1 Back     alignment and function description
>sp|P70280|VAMP7_MOUSE Vesicle-associated membrane protein 7 OS=Mus musculus GN=Vamp7 PE=1 SV=1 Back     alignment and function description
>sp|P47192|VA722_ARATH Vesicle-associated membrane protein 722 OS=Arabidopsis thaliana GN=VAMP722 PE=2 SV=2 Back     alignment and function description
>sp|Q5ZL74|VAMP7_CHICK Vesicle-associated membrane protein 7 OS=Gallus gallus GN=VAMP7 PE=2 SV=1 Back     alignment and function description
>sp|P51809|VAMP7_HUMAN Vesicle-associated membrane protein 7 OS=Homo sapiens GN=VAMP7 PE=1 SV=3 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query202
255548872220 Vesicle-associated membrane protein, put 0.945 0.868 0.937 1e-102
224141911220 predicted protein [Populus trichocarpa] 0.945 0.868 0.921 1e-101
356501396219 PREDICTED: vesicle-associated membrane p 0.945 0.872 0.910 1e-99
225430324220 PREDICTED: vesicle-associated membrane p 0.985 0.904 0.847 3e-99
224089278220 predicted protein [Populus trichocarpa] 0.945 0.868 0.905 5e-99
444436404223 VAMP7-like protein [Eucalyptus cladocaly 0.925 0.838 0.925 3e-98
449437158219 PREDICTED: vesicle-associated membrane p 0.985 0.908 0.828 6e-98
388492222219 unknown [Lotus japonicus] 0.935 0.863 0.894 9e-98
357493899219 Vesicle-associated membrane protein 7C [ 0.985 0.908 0.814 5e-97
15238971221 vesicle-associated membrane protein 713 0.965 0.882 0.826 9e-94
>gi|255548872|ref|XP_002515492.1| Vesicle-associated membrane protein, putative [Ricinus communis] gi|223545436|gb|EEF46941.1| Vesicle-associated membrane protein, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  375 bits (963), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 179/191 (93%), Positives = 188/191 (98%)

Query: 1   MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDG 60
           MAIL++LVARGSVVLAE +ATATNASAIARQIL+KIPGNNDSHVSYSQDRYIFHVKRTDG
Sbjct: 1   MAILYALVARGSVVLAEFTATATNASAIARQILEKIPGNNDSHVSYSQDRYIFHVKRTDG 60

Query: 61  LTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSD 120
           LTVLCMADDTAGRRIPFAFLEDIHQRFV+TYGRAV SAQAY MNDEFSRVL+QQMEYYS+
Sbjct: 61  LTVLCMADDTAGRRIPFAFLEDIHQRFVRTYGRAVHSAQAYAMNDEFSRVLNQQMEYYSN 120

Query: 121 DPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRFR 180
           DPNADRINR+KGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRFR
Sbjct: 121 DPNADRINRLKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRFR 180

Query: 181 STVWWRNVKLT 191
           +TVWWRNVKLT
Sbjct: 181 NTVWWRNVKLT 191

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224141911|ref|XP_002324304.1| predicted protein [Populus trichocarpa] gi|118482139|gb|ABK93000.1| unknown [Populus trichocarpa] gi|222865738|gb|EEF02869.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356501396|ref|XP_003519511.1| PREDICTED: vesicle-associated membrane protein 713-like [Glycine max] Back     alignment and taxonomy information
>gi|225430324|ref|XP_002285207.1| PREDICTED: vesicle-associated membrane protein 713 [Vitis vinifera] gi|296082055|emb|CBI21060.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224089278|ref|XP_002308673.1| predicted protein [Populus trichocarpa] gi|118487208|gb|ABK95432.1| unknown [Populus trichocarpa] gi|222854649|gb|EEE92196.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|444436404|gb|AGE09570.1| VAMP7-like protein [Eucalyptus cladocalyx] Back     alignment and taxonomy information
>gi|449437158|ref|XP_004136359.1| PREDICTED: vesicle-associated membrane protein 713-like [Cucumis sativus] gi|449516866|ref|XP_004165467.1| PREDICTED: vesicle-associated membrane protein 713-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|388492222|gb|AFK34177.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|357493899|ref|XP_003617238.1| Vesicle-associated membrane protein 7C [Medicago truncatula] gi|355518573|gb|AET00197.1| Vesicle-associated membrane protein 7C [Medicago truncatula] Back     alignment and taxonomy information
>gi|15238971|ref|NP_196676.1| vesicle-associated membrane protein 713 [Arabidopsis thaliana] gi|27805763|sp|Q9LFP1.1|VA713_ARATH RecName: Full=Vesicle-associated membrane protein 713; Short=AtVAMP713 gi|8953377|emb|CAB96650.1| putative protein [Arabidopsis thaliana] gi|20259407|gb|AAM14024.1| unknown protein [Arabidopsis thaliana] gi|21689691|gb|AAM67467.1| unknown protein [Arabidopsis thaliana] gi|332004256|gb|AED91639.1| vesicle-associated membrane protein 713 [Arabidopsis thaliana] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query202
TAIR|locus:2147952221 VAMP713 "AT5G11150" [Arabidops 0.965 0.882 0.826 3e-85
TAIR|locus:2116672219 VAMP711 "vesicle-associated me 0.965 0.890 0.825 4.9e-85
TAIR|locus:2059591219 VAMP712 "vesicle-associated me 0.965 0.890 0.810 3.4e-84
TAIR|locus:2176342221 VAMP714 "AT5G22360" [Arabidops 0.975 0.891 0.587 3.8e-62
DICTYBASE|DDB_G0277173260 vamp7B "vesicle-associated mem 0.955 0.742 0.456 6.4e-44
FB|FBgn0033452218 CG1599 [Drosophila melanogaste 0.955 0.885 0.369 3.5e-36
RGD|621558220 Vamp7 "vesicle-associated memb 0.995 0.913 0.366 1.9e-35
MGI|MGI:1096399220 Vamp7 "vesicle-associated memb 0.995 0.913 0.356 3.1e-35
ZFIN|ZDB-GENE-040426-1055220 sybl1 "synaptobrevin-like 1" [ 0.960 0.881 0.384 6.5e-35
UNIPROTKB|Q17QI5220 VAMP7 "Vesicle-associated memb 0.995 0.913 0.361 1.1e-34
TAIR|locus:2147952 VAMP713 "AT5G11150" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 853 (305.3 bits), Expect = 3.0e-85, P = 3.0e-85
 Identities = 162/196 (82%), Positives = 187/196 (95%)

Query:     1 MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNN-DSHVSYSQDRYIFHVKRTD 59
             MAI+F+LVARG+VVL+E SAT+TNAS+I++QIL+K+PGN+ DSH+SYSQDRYIFHVKRTD
Sbjct:     1 MAIIFALVARGTVVLSEFSATSTNASSISKQILEKLPGNDSDSHMSYSQDRYIFHVKRTD 60

Query:    60 GLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYS 119
             GLTVLCMAD+TAGR IPFAFL+DIHQRFVKTYGRA+ SAQAY MNDEFSRVLSQQME+YS
Sbjct:    61 GLTVLCMADETAGRNIPFAFLDDIHQRFVKTYGRAIHSAQAYSMNDEFSRVLSQQMEFYS 120

Query:   120 DDPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRF 179
             +DPNADR++RIKGEMSQVRNVMIENIDKVL+RG+RLELLVDKT NMQGNTFRFRKQARR+
Sbjct:   121 NDPNADRMSRIKGEMSQVRNVMIENIDKVLDRGERLELLVDKTENMQGNTFRFRKQARRY 180

Query:   180 RSTVWWRNVKLTYVLL 195
             R+ +WWRNVKLT  L+
Sbjct:   181 RTIMWWRNVKLTIALI 196
GO:0003674 "molecular_function" evidence=ND
GO:0006810 "transport" evidence=IEA
GO:0016020 "membrane" evidence=ISS
GO:0016021 "integral to membrane" evidence=IEA
GO:0016192 "vesicle-mediated transport" evidence=IEA
GO:0005773 "vacuole" evidence=IDA
GO:0005774 "vacuolar membrane" evidence=TAS
GO:0009651 "response to salt stress" evidence=IMP
GO:0005794 "Golgi apparatus" evidence=IDA
TAIR|locus:2116672 VAMP711 "vesicle-associated membrane protein 711" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2059591 VAMP712 "vesicle-associated membrane protein 712" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2176342 VAMP714 "AT5G22360" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0277173 vamp7B "vesicle-associated membrane protein 7B" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
FB|FBgn0033452 CG1599 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
RGD|621558 Vamp7 "vesicle-associated membrane protein 7" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
MGI|MGI:1096399 Vamp7 "vesicle-associated membrane protein 7" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-040426-1055 sybl1 "synaptobrevin-like 1" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|Q17QI5 VAMP7 "Vesicle-associated membrane protein 7" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q9JHW5VAMP7_RATNo assigned EC number0.38740.94050.8636yesno
P51809VAMP7_HUMANNo assigned EC number0.38210.94050.8636yesno
Q17QI5VAMP7_BOVINNo assigned EC number0.38210.94050.8636yesno
Q9SIQ9VA712_ARATHNo assigned EC number0.82010.93560.8630nono
Q5ZL74VAMP7_CHICKNo assigned EC number0.38210.94050.8636yesno
Q5RF94VAMP7_PONABNo assigned EC number0.37690.94050.8636yesno
Q9LFP1VA713_ARATHNo assigned EC number0.82650.96530.8823yesno
O49377VA711_ARATHNo assigned EC number0.83590.93560.8630nono
P70280VAMP7_MOUSENo assigned EC number0.37690.94050.8636yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
estExt_Genewise1_v1.C_LG_XVIII1645
SubName- Full=Putative uncharacterized protein; (220 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query202
pfam0095789 pfam00957, Synaptobrevin, Synaptobrevin 1e-28
pfam1377482 pfam13774, Longin, Regulated-SNARE-like domain 3e-26
COG5143190 COG5143, SNC1, Synaptobrevin/VAMP-like protein [In 2e-17
>gnl|CDD|201526 pfam00957, Synaptobrevin, Synaptobrevin Back     alignment and domain information 
 Score =  102 bits (256), Expect = 1e-28
 Identities = 35/69 (50%), Positives = 57/69 (82%)

Query: 123 NADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRFRST 182
           + D++N+I+ ++ +V+++M ENIDKVLERG++L+LLVDKT N+Q +  +FRKQAR+ +  
Sbjct: 1   SNDKLNKIQAQVDEVKDIMTENIDKVLERGEKLDLLVDKTENLQSSAQQFRKQARKLKRK 60

Query: 183 VWWRNVKLT 191
           +WW+N+KL 
Sbjct: 61  MWWKNMKLK 69

Length = 89
>gnl|CDD|222370 pfam13774, Longin, Regulated-SNARE-like domain Back     alignment and domain information
>gnl|CDD|227472 COG5143, SNC1, Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 202
KOG0859217 consensus Synaptobrevin/VAMP-like protein [Intrace 100.0
KOG0862216 consensus Synaptobrevin/VAMP-like protein SEC22 [I 100.0
KOG0861198 consensus SNARE protein YKT6, synaptobrevin/VAMP s 100.0
KOG0860116 consensus Synaptobrevin/VAMP-like protein [Intrace 99.96
COG5143190 SNC1 Synaptobrevin/VAMP-like protein [Intracellula 99.94
PF0095789 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 99.93
PF1377483 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3 99.8
COG5143190 SNC1 Synaptobrevin/VAMP-like protein [Intracellula 97.64
PF04086279 SRP-alpha_N: Signal recognition particle, alpha su 95.1
PF09426141 Nyv1_N: Vacuolar R-SNARE Nyv1 N terminal; InterPro 94.71
KOG0811269 consensus SNARE protein PEP12/VAM3/Syntaxin 7/Synt 92.88
PF0390892 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membr 92.39
PF0095789 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 92.24
KOG0810297 consensus SNARE protein Syntaxin 1 and related pro 90.51
PF04099142 Sybindin: Sybindin-like family ; InterPro: IPR0072 90.38
PF0390892 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membr 89.93
KOG0781 587 consensus Signal recognition particle receptor, al 89.37
KOG0938 446 consensus Adaptor complexes medium subunit family 89.1
KOG1983993 consensus Tomosyn and related SNARE-interacting pr 89.1
PF01217141 Clat_adaptor_s: Clathrin adaptor complex small cha 88.8
COG5325283 t-SNARE complex subunit, syntaxin [Intracellular t 87.44
COG5074280 t-SNARE complex subunit, syntaxin [Intracellular t 87.29
PF04628132 Sedlin_N: Sedlin, N-terminal conserved region; Int 83.85
PF04799171 Fzo_mitofusin: fzo-like conserved region; InterPro 82.04
PF09753251 Use1: Membrane fusion protein Use1; InterPro: IPR0 81.39
PF06008264 Laminin_I: Laminin Domain I; InterPro: IPR009254 L 80.7
KOG2635 512 consensus Medium subunit of clathrin adaptor compl 80.42
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information 
Probab=100.00  E-value=1e-63  Score=374.87  Aligned_cols=202  Identities=49%  Similarity=0.860  Sum_probs=195.8

Q ss_pred             CceEEEEEEeCCeEEEeecCCCCCHHHHHHHHhccCCCCCCCceEEeeCCEEEEEEEeCCEEEEEEEcCCCCcccHHHHH
Q 028882            1 MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFL   80 (202)
Q Consensus         1 M~I~Ya~Iar~~~iLae~~~~~~~~~~~a~~vL~ki~~~~~~k~~~~~~~~~fh~l~~~~~~~~~vt~~~~~~~~a~~fL   80 (202)
                      |+|+|++||||++|||||++.+|||..++.++|+++|+.+++|.+|+.|+|.|||+.+||++|+|++|.+.++++||.||
T Consensus         1 m~iiYs~VARGTvvLaeft~~~gNf~sva~qiL~klp~~~n~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaFL   80 (217)
T KOG0859|consen    1 MSIIYSFVARGTVILAEFTEFSGNFSSIAAQILQKLPSSSNSKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAFL   80 (217)
T ss_pred             CceeEEEEecceEEEEeeeeccCCHHHHHHHHHHhCCCCCCCceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHHH
Confidence            89999999999999999999999999999999999996667899999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhhchhhhcccccCCCchhhhHHHHHhhhhcCCccchhHHHHHHHHHHHHHHHHHhHHHHHHhccchhHHHh
Q 028882           81 EDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVD  160 (202)
Q Consensus        81 ~~i~~~f~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~y~~~~~~dkl~~~~~~v~~v~~im~~Ni~~~l~Rge~l~~L~~  160 (202)
                      ++|++.|.+.|+....++.+|+++..|++.|++.|+.|.++|.-|++.+++.+++|+|++|.||||++++|||+||.|++
T Consensus        81 e~Ik~~F~k~YG~~a~ta~AysmN~EFs~vL~qqm~y~s~~p~id~lskvkaqv~evk~vM~eNIekvldRGekiELLVd  160 (217)
T KOG0859|consen   81 ERIKEDFKKRYGGGAHTAVAYSMNKEFSSVLKQQMQYCSEHPEISKLAKVKAQVTEVKGVMMENIEKVLDRGEKIELLVD  160 (217)
T ss_pred             HHHHHHHHHHhccchhHHHHhHhHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHHHHHHHHHHHHHhccCeEEeeec
Confidence            99999999999988888899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHhhHHHHhhhhheeeC
Q 028882          161 KTANMQGNTFRFRKQARRFRSTVWWRNVKLTYVLLADTCLYL  202 (202)
Q Consensus       161 ks~~L~~~s~~f~~~s~~l~r~~~w~~~k~~iii~~~~~~~~  202 (202)
                      ||++|+.+|..|++++++++|+|||+|.|+++++++++++++
T Consensus       161 KTenl~~~s~~fr~q~r~~~r~mw~~n~kl~~iv~~~~~~~i  202 (217)
T KOG0859|consen  161 KTENLRSKSFDFRTQGRKLRRKMWFQNMKLKLIVLGVSISLI  202 (217)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHHHHHhccceehhhhhHHHHHH
Confidence            999999999999999999999999999999999988877653

>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion] Back     alignment and domain information
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis Back     alignment and domain information
>PF13774 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3BW6_A 1H8M_A 3EGX_C 2NUP_C 3EGD_C 2NUT_C 3KYQ_A 1IFQ_B 2VX8_D Back     alignment and domain information
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion] Back     alignment and domain information
>PF04086 SRP-alpha_N: Signal recognition particle, alpha subunit, N-terminal; InterPro: IPR007222 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ] Back     alignment and domain information
>PF09426 Nyv1_N: Vacuolar R-SNARE Nyv1 N terminal; InterPro: IPR019005 This entry represents the N-terminal domain of vacuolar R-SNARE Nyv1, which adopts a longin fold [] Back     alignment and domain information
>KOG0811 consensus SNARE protein PEP12/VAM3/Syntaxin 7/Syntaxin 17 [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway Back     alignment and domain information
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis Back     alignment and domain information
>KOG0810 consensus SNARE protein Syntaxin 1 and related proteins [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>PF04099 Sybindin: Sybindin-like family ; InterPro: IPR007233 Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses Back     alignment and domain information
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway Back     alignment and domain information
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>KOG1983 consensus Tomosyn and related SNARE-interacting proteins [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment Back     alignment and domain information
>COG5325 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion] Back     alignment and domain information
>COG5074 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion] Back     alignment and domain information
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport Back     alignment and domain information
>PF04799 Fzo_mitofusin: fzo-like conserved region; InterPro: IPR006884 This entry represents the heptad repeat domain which is conserved at the C terminus of Fzo/mitofusion family of GTPases Back     alignment and domain information
>PF09753 Use1: Membrane fusion protein Use1; InterPro: IPR019150 This entry represents a family of proteins, approximately 300 residues in length, involved in vesicle transport Back     alignment and domain information
>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells Back     alignment and domain information
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query202
4b93_A189 Complex Of Vamp7 Cytoplasmic Domain With 2nd Ankyri 3e-36
2dmw_A131 Solution Structure Of The Longin Domain Of Synaptob 6e-22
4afi_A173 Complex Between Vamp7 Longin Domain And Fragment Of 3e-21
2vx8_A169 Vamp7 Longin Domain Hrb Peptide Complex Length = 16 5e-20
2nup_C196 Crystal Structure Of The Human Sec23a24A HETERODIME 3e-11
2nps_A74 Crystal Structure Of The Early Endosomal Snare Comp 1e-09
3kyq_A199 Lipid-Induced Conformational Switch Controls Fusion 2e-07
3egd_C157 Crystal Structure Of The Mammalian Copii-Coat Prote 7e-07
3hd7_A91 Helical Extension Of The Neuronal Snare Complex Int 1e-06
2kog_A119 Lipid-Bound Synaptobrevin Solution Nmr Structure Le 1e-06
1sfc_A96 Neuronal Synaptic Fusion Complex Length = 96 9e-06
1l4a_A80 X-Ray Structure Of The Neuronal ComplexinSNARE COMP 2e-05
1kil_A66 Three-Dimensional Structure Of The ComplexinSNARE C 7e-05
1gl2_A65 Crystal Structure Of An Endosomal Snare Core Comple 4e-04
3b5n_A61 Structure Of The Yeast Plasma Membrane Snare Comple 6e-04
>pdb|4B93|A Chain A, Complex Of Vamp7 Cytoplasmic Domain With 2nd Ankyrin Repeat Domain Of Varp Length = 189 Back     alignment and structure 
Iteration: 1

 Score =  147 bits (372), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 70/189 (37%), Positives = 117/189 (61%), Gaps = 1/189 (0%)
Query: 1   MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDG 60
           MAILF++VARG+ +LA+ +    N   +  QIL KIP  N+  ++YS   Y+FH    D 
Sbjct: 2   MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNK-LTYSHGNYLFHYICQDR 60
Query: 61  LTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSD 120
           +  LC+ DD   R   F+FL ++ +RF  TYG    +A  Y MN EFS VL+ Q++++S+
Sbjct: 61  IVYLCITDDDFERSRAFSFLNEVKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHSE 120
Query: 121 DPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFRKQARRFR 180
           + + D++   + ++ +++ +M+ NID V +RG+RLELL+DKT N+  ++  F+  +R   
Sbjct: 121 NKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLIDKTENLVDSSVTFKTTSRNLA 180
Query: 181 STVWWRNVK 189
             +  +N+K
Sbjct: 181 RAMCMKNIK 189
>pdb|2DMW|A Chain A, Solution Structure Of The Longin Domain Of Synaptobrevin- Like Protein 1 Length = 131 Back     alignment and structure
>pdb|4AFI|A Chain A, Complex Between Vamp7 Longin Domain And Fragment Of Delta- Adaptin From Ap3 Length = 173 Back     alignment and structure
>pdb|2VX8|A Chain A, Vamp7 Longin Domain Hrb Peptide Complex Length = 169 Back     alignment and structure
>pdb|2NUP|C Chain C, Crystal Structure Of The Human Sec23a24A HETERODIMER, Complexed With The Snare Protein Sec22b Length = 196 Back     alignment and structure
>pdb|2NPS|A Chain A, Crystal Structure Of The Early Endosomal Snare Complex Length = 74 Back     alignment and structure
>pdb|3KYQ|A Chain A, Lipid-Induced Conformational Switch Controls Fusion Activity Of Longin Domain Snare Ykt6 Length = 199 Back     alignment and structure
>pdb|3EGD|C Chain C, Crystal Structure Of The Mammalian Copii-Coat Protein Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22 AND BOUND To The Transport Signal Sequence Of Vesicular Stomatitis Virus Glycoprotein Length = 157 Back     alignment and structure
>pdb|3HD7|A Chain A, Helical Extension Of The Neuronal Snare Complex Into The Membrane, Spacegroup C 1 2 1 Length = 91 Back     alignment and structure
>pdb|2KOG|A Chain A, Lipid-Bound Synaptobrevin Solution Nmr Structure Length = 119 Back     alignment and structure
>pdb|1SFC|A Chain A, Neuronal Synaptic Fusion Complex Length = 96 Back     alignment and structure
>pdb|1L4A|A Chain A, X-Ray Structure Of The Neuronal ComplexinSNARE COMPLEX From The Squid Loligo Pealei Length = 80 Back     alignment and structure
>pdb|1KIL|A Chain A, Three-Dimensional Structure Of The ComplexinSNARE COMPLEX Length = 66 Back     alignment and structure
>pdb|1GL2|A Chain A, Crystal Structure Of An Endosomal Snare Core Complex Length = 65 Back     alignment and structure
>pdb|3B5N|A Chain A, Structure Of The Yeast Plasma Membrane Snare Complex Length = 61 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query202
2nut_C196 Vesicle-trafficking protein SEC22B; human copii SE 4e-48
4afi_A173 AP-3 complex subunit delta-1, vesicle-associated p 1e-43
2vx8_A169 Nucleoporin-like protein RIP, vesicle-associated m 2e-41
3kyq_A199 YKT6, synaptobrevin homolog YKT6; V-snare homolog, 6e-36
1sfc_A96 VAMP 2, protein (synaptobrevin 2); membrane fusion 7e-26
2kog_A119 Vesicle-associated membrane protein 2; synaptobrev 9e-26
2nps_A74 VAMP-4, vesicle-associated membrane protein 4; ves 2e-25
1l4a_A80 Synaptobrevin; snare, snare complex, membrane fusi 3e-25
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 6e-23
3b5n_A61 Synaptobrevin homolog 1; snare complex, syntaxin, 2e-20
1n7s_A63 Vesicle-associated membrane protein 2; neuronal sn 7e-20
1gl2_A65 Endobrevin; membrane protein, membrane fusion prot 1e-18
3bw6_A144 Synaptobrevin homolog YKT6; YKT6P, farnesylation, 5e-07
1urq_A63 M-tomosyn isoform; transport protein, tomosyn-snar 6e-05
>2nut_C Vesicle-trafficking protein SEC22B; human copii SEC23/24 complexed with SEC22, protein transport; 2.30A {Homo sapiens} PDB: 2nup_C 3egd_C 3egx_C 1ifq_A Length = 196 Back     alignment and structure
 Score =  155 bits (391), Expect = 4e-48
 Identities = 40/193 (20%), Positives = 86/193 (44%), Gaps = 9/193 (4%)

Query: 3   ILFSLVARGSVVLAECSATATNASA---------IARQILDKIPGNNDSHVSYSQDRYIF 53
           +L +++AR +  L   ++   +  +          A+Q+  K+   + +  +       F
Sbjct: 3   VLLTMIARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMTF 62

Query: 54  HVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQ 113
           H     G+  L + +    +++ FA+LED+H  F + +G+ V +        EF   + +
Sbjct: 63  HYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQK 122

Query: 114 QMEYYSDDPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVDKTANMQGNTFRFR 173
             + Y D      +  I  E+  V+ +M+ NI++VL+RG+ L  L  K  N+   + ++R
Sbjct: 123 TKKLYIDSRARRNLGSINTELQDVQRIMVANIEEVLQRGEALSALDSKANNLSSLSKKYR 182

Query: 174 KQARRFRSTVWWR 186
           + A+       + 
Sbjct: 183 QDAKYLNMRSTYA 195
>4afi_A AP-3 complex subunit delta-1, vesicle-associated protein 7; endocytosis, exocytosis, clathrin adaptor, chimera, fusion P; 2.80A {Homo sapiens} Length = 173 Back     alignment and structure
>2vx8_A Nucleoporin-like protein RIP, vesicle-associated membrane protein 7; endocytosis,exocytosis, endocytosis, exocytosis, acetylation, coiled coil; 2.2A {Homo sapiens} PDB: 2dmw_A Length = 169 Back     alignment and structure
>3kyq_A YKT6, synaptobrevin homolog YKT6; V-snare homolog, lipid binding, cytoplasmic vesicle, ER-GOLG transport, golgi apparatus, lipoprotein; HET: DPV; 2.44A {Rattus norvegicus} Length = 199 Back     alignment and structure
>1sfc_A VAMP 2, protein (synaptobrevin 2); membrane fusion protein complex, transport protein; 2.40A {Rattus norvegicus} SCOP: h.1.15.1 Length = 96 Back     alignment and structure
>2kog_A Vesicle-associated membrane protein 2; synaptobrevin, VAMP2, DPC micelle, snare, coiled coil, membrane fusion, transmembrane; NMR {Rattus norvegicus} Length = 119 Back     alignment and structure
>2nps_A VAMP-4, vesicle-associated membrane protein 4; vesicle fusion, snare complex, early endosomal snare complex, VTI1A, VAMP4, transport protein; 2.50A {Mus musculus} Length = 74 Back     alignment and structure
>1l4a_A Synaptobrevin; snare, snare complex, membrane fusion, neurotransmission, endocytosis/exocytosis complex; 2.95A {Loligo pealei} SCOP: h.1.15.1 Length = 80 Back     alignment and structure
>3hd7_A Vesicle-associated membrane protein 2; membrane protein, coiled-coil, 4-helical bundle, cell juncti cytoplasmic vesicle, membrane, phosphoprotein; HET: GGG; 3.40A {Rattus norvegicus} PDB: 3hd9_A 3ipd_A Length = 91 Back     alignment and structure
>3b5n_A Synaptobrevin homolog 1; snare complex, syntaxin, synaptobrevin, SNAP-25, SSO1P, SNC1P, SEC9P, SSO1, SNC1, coiled coil; 1.60A {Saccharomyces cerevisiae} SCOP: h.1.15.1 Length = 61 Back     alignment and structure
>1n7s_A Vesicle-associated membrane protein 2; neuronal snare protein complex, four helix bundle, transport protein; 1.45A {Rattus norvegicus} SCOP: h.1.15.1 PDB: 1kil_A 3rk2_A 3rk3_A 3rl0_A 3fii_B 3g94_B Length = 63 Back     alignment and structure
>1gl2_A Endobrevin; membrane protein, membrane fusion protein complex, coiled coil, transmembrane; 1.9A {Rattus norvegicus} SCOP: h.1.15.1 Length = 65 Back     alignment and structure
>3bw6_A Synaptobrevin homolog YKT6; YKT6P, farnesylation, vacuole fusion, snare, coiled coil, lipoprotein, membrane, phosphoprotein; 2.50A {Saccharomyces cerevisiae} PDB: 1h8m_A 1iou_A Length = 144 Back     alignment and structure
>1urq_A M-tomosyn isoform; transport protein, tomosyn-snare complex, exocytosis, four helical bundle, coiled coil; 2.0A {Rattus norvegicus} SCOP: h.1.15.1 Length = 63 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query202
4b93_A189 Vesicle-associated membrane protein 7; endocytosis 100.0
2nut_C196 Vesicle-trafficking protein SEC22B; human copii SE 100.0
3kyq_A199 YKT6, synaptobrevin homolog YKT6; V-snare homolog, 100.0
4afi_A173 AP-3 complex subunit delta-1, vesicle-associated p 100.0
2vx8_A169 Nucleoporin-like protein RIP, vesicle-associated m 99.97
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 99.96
2kog_A119 Vesicle-associated membrane protein 2; synaptobrev 99.95
2nps_A74 VAMP-4, vesicle-associated membrane protein 4; ves 99.93
1sfc_A96 VAMP 2, protein (synaptobrevin 2); membrane fusion 99.93
1l4a_A80 Synaptobrevin; snare, snare complex, membrane fusi 99.92
3bw6_A144 Synaptobrevin homolog YKT6; YKT6P, farnesylation, 99.91
1n7s_A63 Vesicle-associated membrane protein 2; neuronal sn 99.88
3b5n_A61 Synaptobrevin homolog 1; snare complex, syntaxin, 99.87
1gl2_A65 Endobrevin; membrane protein, membrane fusion prot 99.82
1urq_A63 M-tomosyn isoform; transport protein, tomosyn-snar 99.73
3fie_C38 Fragment of vesicle-associated membrane protein 2; 98.34
3zym_A310 Phosphatidylinositol-binding clathrin assembly PR 98.28
2fh5_A185 Signal recognition particle receptor alpha subunit 97.86
3hd7_B109 Syntaxin-1A; membrane protein, coiled-coil, 4-heli 96.64
2fz0_A149 R-snare NYV1P, V-snare component of the vacuolar s 94.96
2j3w_A142 Sedlin, trafficking protein particle complex prote 94.5
2j3t_C145 Trafficking protein particle complex subunit 1, tr 94.0
1w63_Q158 Adapter-related protein complex 1 sigma 1A subunit 91.06
2vgl_S142 AP-2 complex subunit sigma-1; cytoplasmic vesicle, 89.74
3tjz_C153 Coatomer subunit zeta-1; protein trafficking, golg 86.97
2j3t_D219 Trafficking protein particle complex subunit 4; tr 84.68
1w63_M 423 Adaptor-related protein complex 1, MU 1 subunit; e 83.44
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 82.35
1jth_B77 Syntaxin 1A; coiled-coil, polar layer, endocytosis 82.13
3cue_A219 Transport protein particle 23 kDa subunit; membran 81.84
3cue_C159 Transport protein particle 18 kDa subunit; membran 81.62
2vgl_M 435 AP-2 complex subunit MU-1; cytoplasmic vesicle, al 80.25
>4b93_A Vesicle-associated membrane protein 7; endocytosis, exocytosis, snare; 2.00A {Mus musculus} PDB: 2dmw_A Back     alignment and structure
Probab=100.00  E-value=3.3e-61  Score=373.01  Aligned_cols=188  Identities=37%  Similarity=0.677  Sum_probs=150.9

Q ss_pred             CceEEEEEEeCCeEEEeecCCCCCHHHHHHHHhccCCCCCCCceEEeeCCEEEEEEEeCCEEEEEEEcCCCCcccHHHHH
Q 028882            1 MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFL   80 (202)
Q Consensus         1 M~I~Ya~Iar~~~iLae~~~~~~~~~~~a~~vL~ki~~~~~~k~~~~~~~~~fh~l~~~~~~~~~vt~~~~~~~~a~~fL   80 (202)
                      |||+|||||||++|||||+..+|||..+++.+|+++| ++++|.++++|+|.|||+.++|++|+|+||.+||+++||.||
T Consensus         2 M~ilYa~VArg~~iLae~t~~~gnf~~ia~~iL~kip-~~~~k~s~~~~~y~fHyl~~~gl~yl~i~d~~yp~r~af~fL   80 (189)
T 4b93_A            2 MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIP-SENNKLTYSHGNYLFHYICQDRIVYLCITDDDFERSRAFSFL   80 (189)
T ss_dssp             CSEEEEEEEETTEEEEEEESSEECHHHHHHHHHTTCC-SSSEEEEEEETTEEEEEEEETTEEEEEEEETTSCHHHHHHHH
T ss_pred             CceEEEEEEeCCEEEEeCCCCCCCHHHHHHHHHHhCC-CCCCeEEEEECCEEEEEEEeCCeEEEEEEcCccCHHHHHHHH
Confidence            9999999999999999999999999999999999999 688999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhhchhhhcccccCCCchhhhHHHHHhhhhcCCccchhHHHHHHHHHHHHHHHHHhHHHHHHhccchhHHHh
Q 028882           81 EDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVRNVMIENIDKVLERGDRLELLVD  160 (202)
Q Consensus        81 ~~i~~~f~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~y~~~~~~dkl~~~~~~v~~v~~im~~Ni~~~l~Rge~l~~L~~  160 (202)
                      ++|.++|...|+....++.++++..+|.+.|+++|++|++.+..|++.+++.+|+||++||.+||+++|+|||+||.|++
T Consensus        81 ~~i~~eF~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~y~d~~~~d~l~~~~~~l~ev~~im~~Ni~~vl~Rge~l~~L~~  160 (189)
T 4b93_A           81 NEVKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHSENKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLID  160 (189)
T ss_dssp             HHHHHHHHHHHGGGGGTCCTTTTHHHHHHHHHHHHHHHHCC-------CCHHHHHTTTTCCEECCCCBCTTSSBCCCCEE
T ss_pred             HHHHHHHHhhccccccccCCccccchhhHHHHHHHHhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHH
Confidence            99999999999987777788888889999999999999766667999999999999999999999999999999999999


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHhh
Q 028882          161 KTANMQGNTFRFRKQARRFRSTVWWRNVK  189 (202)
Q Consensus       161 ks~~L~~~s~~f~~~s~~l~r~~~w~~~k  189 (202)
                      ||++|+.+|..|+++|++|+|+|||+|+|
T Consensus       161 ks~~L~~~s~~f~~~a~~l~r~mwwkn~K  189 (189)
T 4b93_A          161 KTENLVDSSVTFKTTSRNLARAMCMKNIK  189 (189)
T ss_dssp             TTCC-------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            99999999999999999999999999987
>2nut_C Vesicle-trafficking protein SEC22B; human copii SEC23/24 complexed with SEC22, protein transport; 2.30A {Homo sapiens} PDB: 2nup_C 3egd_C 3egx_C 1ifq_A Back     alignment and structure
>3kyq_A YKT6, synaptobrevin homolog YKT6; V-snare homolog, lipid binding, cytoplasmic vesicle, ER-GOLG transport, golgi apparatus, lipoprotein; HET: DPV; 2.44A {Rattus norvegicus} Back     alignment and structure
>4afi_A AP-3 complex subunit delta-1, vesicle-associated protein 7; endocytosis, exocytosis, clathrin adaptor, chimera, fusion P; 2.80A {Homo sapiens} Back     alignment and structure
>2vx8_A Nucleoporin-like protein RIP, vesicle-associated membrane protein 7; endocytosis,exocytosis, endocytosis, exocytosis, acetylation, coiled coil; 2.2A {Homo sapiens} PDB: 2dmw_A Back     alignment and structure
>3hd7_A Vesicle-associated membrane protein 2; membrane protein, coiled-coil, 4-helical bundle, cell juncti cytoplasmic vesicle, membrane, phosphoprotein; HET: GGG; 3.40A {Rattus norvegicus} PDB: 3hd9_A 3ipd_A Back     alignment and structure
>2kog_A Vesicle-associated membrane protein 2; synaptobrevin, VAMP2, DPC micelle, snare, coiled coil, membrane fusion, transmembrane; NMR {Rattus norvegicus} Back     alignment and structure
>2nps_A VAMP-4, vesicle-associated membrane protein 4; vesicle fusion, snare complex, early endosomal snare complex, VTI1A, VAMP4, transport protein; 2.50A {Mus musculus} Back     alignment and structure
>1sfc_A VAMP 2, protein (synaptobrevin 2); membrane fusion protein complex, transport protein; 2.40A {Rattus norvegicus} SCOP: h.1.15.1 Back     alignment and structure
>1l4a_A Synaptobrevin; snare, snare complex, membrane fusion, neurotransmission, endocytosis/exocytosis complex; 2.95A {Loligo pealei} SCOP: h.1.15.1 Back     alignment and structure
>3bw6_A Synaptobrevin homolog YKT6; YKT6P, farnesylation, vacuole fusion, snare, coiled coil, lipoprotein, membrane, phosphoprotein; 2.50A {Saccharomyces cerevisiae} PDB: 1h8m_A 1iou_A Back     alignment and structure
>1n7s_A Vesicle-associated membrane protein 2; neuronal snare protein complex, four helix bundle, transport protein; 1.45A {Rattus norvegicus} SCOP: h.1.15.1 PDB: 1kil_A 3rk2_A 3rk3_A 3rl0_A 3fii_B 3g94_B Back     alignment and structure
>3b5n_A Synaptobrevin homolog 1; snare complex, syntaxin, synaptobrevin, SNAP-25, SSO1P, SNC1P, SEC9P, SSO1, SNC1, coiled coil; 1.60A {Saccharomyces cerevisiae} SCOP: h.1.15.1 Back     alignment and structure
>1gl2_A Endobrevin; membrane protein, membrane fusion protein complex, coiled coil, transmembrane; 1.9A {Rattus norvegicus} SCOP: h.1.15.1 Back     alignment and structure
>1urq_A M-tomosyn isoform; transport protein, tomosyn-snare complex, exocytosis, four helical bundle, coiled coil; 2.0A {Rattus norvegicus} SCOP: h.1.15.1 Back     alignment and structure
>3fie_C Fragment of vesicle-associated membrane protein 2; BONT F, VAMP, inhibitor, complex structure, acetylation, cell junction, hydrolase; 2.10A {Clostridium botulinum} Back     alignment and structure
>3zym_A Phosphatidylinositol-binding clathrin assembly PR vesicle-associated membrane protein...; endocytosis, synaptobrevin, VAMP2, VAMP3, AP180; HET: PO4; 2.03A {Rattus norvegicus} Back     alignment and structure
>2fh5_A Signal recognition particle receptor alpha subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Homo sapiens} SCOP: d.110.4.4 PDB: 2go5_1 Back     alignment and structure
>3hd7_B Syntaxin-1A; membrane protein, coiled-coil, 4-helical bundle, cell juncti cytoplasmic vesicle, membrane, phosphoprotein; HET: GGG; 3.40A {Rattus norvegicus} PDB: 3hd9_B 3ipd_B Back     alignment and structure
>2fz0_A R-snare NYV1P, V-snare component of the vacuolar snare complex involved in vesicle fusion; inhibits...; snare protein, longin domain; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>2j3w_A Sedlin, trafficking protein particle complex protein 2; multisubunit tethering factor, trapp, palmitate, transport, lipoprotein; HET: PLM; 2.1A {Mus musculus} SCOP: d.110.4.3 PDB: 1h3q_A Back     alignment and structure
>2j3t_C Trafficking protein particle complex subunit 1, trafficking protein particle complex subunit 3; trapp, palmitate, transport, lipoprotein, ER-golgi transport apparatus, protein transport; HET: PLM; 2.4A {Mus musculus} Back     alignment and structure
>1w63_Q Adapter-related protein complex 1 sigma 1A subunit; endocytosis, clathrin adaptor, transport, coated PITS; 4.0A {Mus musculus} SCOP: i.23.1.1 Back     alignment and structure
>2vgl_S AP-2 complex subunit sigma-1; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Mus musculus} SCOP: i.23.1.1 PDB: 2jkt_I 2jkr_I* 2xa7_S Back     alignment and structure
>3tjz_C Coatomer subunit zeta-1; protein trafficking, golgi membrane, protein transport-prote binding complex; HET: GNP; 2.90A {Bos taurus} PDB: 2hf6_A Back     alignment and structure
>2j3t_D Trafficking protein particle complex subunit 4; trapp, palmitate, transport, lipoprotein, ER-golgi transport apparatus, protein transport; HET: PLM; 2.4A {Homo sapiens} PDB: 2zmv_A 2jsn_A Back     alignment and structure
>1w63_M Adaptor-related protein complex 1, MU 1 subunit; endocytosis, clathrin adaptor, transport, coated PITS; 4.0A {Mus musculus} SCOP: i.23.1.1 Back     alignment and structure
>3hd7_A Vesicle-associated membrane protein 2; membrane protein, coiled-coil, 4-helical bundle, cell juncti cytoplasmic vesicle, membrane, phosphoprotein; HET: GGG; 3.40A {Rattus norvegicus} PDB: 3hd9_A 3ipd_A Back     alignment and structure
>1jth_B Syntaxin 1A; coiled-coil, polar layer, endocytosis-exocytosis complex; 2.00A {Rattus norvegicus} SCOP: h.1.15.1 PDB: 1hvv_A* 1urq_B Back     alignment and structure
>3cue_A Transport protein particle 23 kDa subunit; membrane traffic, GEF, tethering complex, RAB activation, GU nucleotide exchange factor; HET: PLM; 3.70A {Saccharomyces cerevisiae} Back     alignment and structure
>3cue_C Transport protein particle 18 kDa subunit; membrane traffic, GEF, tethering complex, RAB activation, GU nucleotide exchange factor; HET: PLM; 3.70A {Saccharomyces cerevisiae} Back     alignment and structure
>2vgl_M AP-2 complex subunit MU-1; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Rattus norvegicus} PDB: 2jkr_M 2jkt_M 2bp5_M* 2xa7_M Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 202
d1ifqa_127 d.110.4.1 (A:) Sec22b {Mouse (Mus musculus) [TaxId 1e-28
d1ioua_140 d.110.4.1 (A:) Synaptobrevin homolog 1 ykt6 {Baker 3e-21
>d1ifqa_ d.110.4.1 (A:) Sec22b {Mouse (Mus musculus) [TaxId: 10090]} Length = 127 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: SNARE-like
family: Synatpobrevin N-terminal domain
domain: Sec22b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  101 bits (254), Expect = 1e-28
 Identities = 24/127 (18%), Positives = 56/127 (44%), Gaps = 11/127 (8%)

Query: 2   AILFSLVARGSVVLAECSATATNASA---------IARQILDKIPGNNDSHVSYSQDRYI 52
           ++L +++AR +  L   ++   +  +          A+Q+  K+   + +  +       
Sbjct: 1   SVLLTMIARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMT 60

Query: 53  FHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSA-QAYGMNDEFSRVL 111
           FH     G+  L + +    +++ FA+LED+H  F + +G+ V +  + Y    EF   +
Sbjct: 61  FHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFI-EFDTFI 119

Query: 112 SQQMEYY 118
            +  + Y
Sbjct: 120 QKTKKLY 126
>d1ioua_ d.110.4.1 (A:) Synaptobrevin homolog 1 ykt6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 140 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query202
d1ifqa_127 Sec22b {Mouse (Mus musculus) [TaxId: 10090]} 99.95
d1ioua_140 Synaptobrevin homolog 1 ykt6 {Baker's yeast (Sacch 99.8
d2fh5a1129 Signal recognition particle receptor alpha subunit 97.99
d2vgls_142 Sigma2 adaptin (clathrin coat assembly protein AP1 95.27
d2j3wa1140 Sedlin (SEDL) {Mouse (Mus musculus) [TaxId: 10090] 93.48
d2vglm2141 Mu2 adaptin (clathrin coat assembly protein AP50) 93.2
>d1ifqa_ d.110.4.1 (A:) Sec22b {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: SNARE-like
family: Synatpobrevin N-terminal domain
domain: Sec22b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.95  E-value=2.6e-27  Score=169.51  Aligned_cols=116  Identities=22%  Similarity=0.451  Sum_probs=103.9

Q ss_pred             ceEEEEEEeC--CeEEEeecCCCCC-------HHHHHHHHhccCCCCCCCceEEeeCCEEEEEEEeCCEEEEEEEcCCCC
Q 028882            2 AILFSLVARG--SVVLAECSATATN-------ASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAG   72 (202)
Q Consensus         2 ~I~Ya~Iar~--~~iLae~~~~~~~-------~~~~a~~vL~ki~~~~~~k~~~~~~~~~fh~l~~~~~~~~~vt~~~~~   72 (202)
                      ||+|++|||+  ++||||+++.+++       +.+.|+.++++++++.++|++++.|+|.|||+.++|++|+|+||.+||
T Consensus         1 sil~t~IaR~~DgL~L~~s~~~~~~~~~~~~~~k~qak~ll~kl~~~~~~r~s~~~~~y~fHy~~~~gi~yl~i~d~~~~   80 (127)
T d1ifqa_           1 SVLLTMIARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMTFHYIIEQGVCYLVLCEAAFP   80 (127)
T ss_dssp             CCCEEEEEETTTCCEEEEECCCTTCCHHHHHHHHHHHHHHHTTCCTTSCSEEEEEETTEEEEEEEETTEEEEEEEETTSC
T ss_pred             CeEEEEEEEecCCcEEEEEeccccccchhHHHHHHHHHHHHHhCCCCCCCcEEEEECCEEEEEEecCCeEEEEEEccccC
Confidence            6899999996  5999999975543       246789999999877789999999999999999999999999999999


Q ss_pred             cccHHHHHHHHHHHHhhhhchhhhcc-cccCCCchhhhHHHHHhhhh
Q 028882           73 RRIPFAFLEDIHQRFVKTYGRAVLSA-QAYGMNDEFSRVLSQQMEYY  118 (202)
Q Consensus        73 ~~~a~~fL~~i~~~f~~~~~~~~~~~-~~~~~~~~f~~~l~~~~~~y  118 (202)
                      +++||.||++|.++|...|+.....+ +||++. +|+..|++.++.|
T Consensus        81 ~~laF~fLeei~~eF~~~y~~~i~~~~rpy~Fi-~Fd~~iqk~k~~y  126 (127)
T d1ifqa_          81 KKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFI-EFDTFIQKTKKLY  126 (127)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTTTTTCCSTTTTG-GGHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhhhhhhhcccCCcchH-HHHHHHHHHHHhc
Confidence            99999999999999999998766554 789985 8999999999988
>d1ioua_ d.110.4.1 (A:) Synaptobrevin homolog 1 ykt6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2fh5a1 d.110.4.4 (A:1-129) Signal recognition particle receptor alpha subunit, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2j3wa1 d.110.4.3 (A:1-140) Sedlin (SEDL) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure