Citrus Sinensis ID: 028846

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---
MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQAQDFRSTGTKMRRKMWLQNMKIKLIVLGILIALILIIVLSVCHGFNCGK
cccccEEEEEEEcccEEEEEEccccccHHHHHHHHHccccccccEEEEEEccEEEEEEEEccEEEEEEEccccccccHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccc
ccccHEEEEEEEcccEEEEEEccccccHHHHHHHHHHHcccccccEEEEcccEEEEEEEcccEEEEEEEccccccccHHHHHHHHHHHHHHHHcccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccc
MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLqklpasnnkftyncdahtfnylvdngYTYCVVadessgrqipmAFLERVKDEfvskygggkaatapanglnkEFGKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQAQDFRSTGTKMRRKMWLQNMKIKLIVLGILIALILIIVLSVchgfncgk
MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDktenlhqqaqdfrstgtkMRRKMWLQNMKIKLIVLGILIALILIIVLSVCHGFNCGK
MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQAQDFRSTGTKMRRKMWLQNMkiklivlgilialiliivlSVCHGFNCGK
*****LIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKT***************KMRRKMWLQNMKIKLIVLGILIALILIIVLSVCHGFNC**
**QKSLIYAFVARGNVVLAEYTEFSGNFNSIAY*CL**********TYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFV*****************************VSEVKGVMMENIEKVLDRGEK**********************TKMRRKMWLQNMKIKLIVLGILIALILIIVLSVCHGFNCG*
MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQAQDFRSTGTKMRRKMWLQNMKIKLIVLGILIALILIIVLSVCHGFNCGK
**QKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQAQDFRSTGTKMRRKMWLQNMKIKLIVLGILIALILIIVLSVCHGFNCGK
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MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQAQDFRSTGTKMRRKMWLQNMKIKLIVLGILIALILIIVLSVCHGFNCGK
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 ?
Query203 2.2.26 [Sep-21-2011]
Q9MAS5220 Putative vesicle-associat yes no 0.990 0.913 0.739 5e-87
Q9ZTW3219 Vesicle-associated membra no no 0.990 0.917 0.762 2e-85
P47192221 Vesicle-associated membra no no 1.0 0.918 0.755 2e-84
O48850285 Vesicle-associated membra no no 0.990 0.705 0.735 8e-82
O23429222 Vesicle-associated membra no no 0.990 0.905 0.631 3e-70
Q9M376240 Vesicle-associated membra no no 0.995 0.841 0.514 2e-65
Q8VY69217 Vesicle-associated membra no no 0.980 0.917 0.615 8e-62
Q9LFP1221 Vesicle-associated membra no no 0.950 0.873 0.380 2e-37
Q9FMR5221 Vesicle-associated membra no no 0.950 0.873 0.342 4e-36
O49377219 Vesicle-associated membra no no 0.950 0.881 0.382 2e-34
>sp|Q9MAS5|VA726_ARATH Putative vesicle-associated membrane protein 726 OS=Arabidopsis thaliana GN=VAMP726 PE=3 SV=2 Back     alignment and function desciption
 Score =  320 bits (819), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 162/219 (73%), Positives = 182/219 (83%), Gaps = 18/219 (8%)

Query: 1   MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVD 60
           M Q+SLIY+FVARG V+LAEYTEF GNF S+A QCLQKLP+SNNKFTYNCD HTFNYL D
Sbjct: 1   MGQQSLIYSFVARGTVILAEYTEFKGNFTSVAAQCLQKLPSSNNKFTYNCDGHTFNYLAD 60

Query: 61  NGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFG--------- 111
           NG+TYCVV  ES+GRQIPMAFLERVK++F  +YGGGKA+TA AN LNKEFG         
Sbjct: 61  NGFTYCVVVIESAGRQIPMAFLERVKEDFNKRYGGGKASTAKANSLNKEFGSKLKEHMQY 120

Query: 112 ---------KLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQAQDFRSTG 162
                    KL+KVKAQV+EVKGVMMENIEKVLDRGEKIELLVDKTENL  QAQDFR+ G
Sbjct: 121 CADHPEEISKLSKVKAQVTEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRTQG 180

Query: 163 TKMRRKMWLQNMKIKLIVLGILIALILIIVLSVCHGFNC 201
           TKM+RK+W +NMKIKLIV GI++ALILII+LSVCHGF C
Sbjct: 181 TKMKRKLWFENMKIKLIVFGIIVALILIIILSVCHGFKC 219
Involved in the targeting and/or fusion of transport vesicles to their target membrane.
Arabidopsis thaliana (taxid: 3702)
>sp|Q9ZTW3|VA721_ARATH Vesicle-associated membrane protein 721 OS=Arabidopsis thaliana GN=VAMP721 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|O48850|VA725_ARATH Vesicle-associated membrane protein 725 OS=Arabidopsis thaliana GN=VAMP725 PE=2 SV=2 Back     alignment and function description
>sp|O23429|VA724_ARATH Vesicle-associated membrane protein 724 OS=Arabidopsis thaliana GN=VAMP724 PE=2 SV=2 Back     alignment and function description
>sp|Q9M376|VA727_ARATH Vesicle-associated membrane protein 727 OS=Arabidopsis thaliana GN=VAMP727 PE=2 SV=1 Back     alignment and function description
>sp|Q8VY69|VA723_ARATH Vesicle-associated membrane protein 723 OS=Arabidopsis thaliana GN=VAMP723 PE=2 SV=1 Back     alignment and function description
>sp|Q9LFP1|VA713_ARATH Vesicle-associated membrane protein 713 OS=Arabidopsis thaliana GN=VAMP713 PE=2 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|O49377|VA711_ARATH Vesicle-associated membrane protein 711 OS=Arabidopsis thaliana GN=VAMP711 PE=2 SV=2 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 ?
Query203
225423676221 PREDICTED: putative vesicle-associated m 1.0 0.918 0.805 1e-101
225423678229 PREDICTED: putative vesicle-associated m 1.0 0.886 0.777 2e-98
427199312219 vesicle-associated membrane protein 72 [ 0.990 0.917 0.844 4e-94
356532974221 PREDICTED: putative vesicle-associated m 1.0 0.918 0.846 4e-94
351727010221 uncharacterized protein LOC100500089 [Gl 1.0 0.918 0.837 4e-93
255638090221 unknown [Glycine max] 1.0 0.918 0.837 1e-92
224115526221 predicted protein [Populus trichocarpa] 1.0 0.918 0.828 3e-92
356532978232 PREDICTED: putative vesicle-associated m 1.0 0.875 0.801 2e-91
255578566221 Vesicle-associated membrane protein, put 1.0 0.918 0.805 3e-91
116781485222 unknown [Picea sitchensis] gi|116791336| 1.0 0.914 0.742 4e-91
>gi|225423676|ref|XP_002276767.1| PREDICTED: putative vesicle-associated membrane protein 726 isoform 1 [Vitis vinifera] gi|147857290|emb|CAN81365.1| hypothetical protein VITISV_015772 [Vitis vinifera] gi|297737980|emb|CBI27181.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  372 bits (954), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 178/221 (80%), Positives = 193/221 (87%), Gaps = 18/221 (8%)

Query: 1   MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVD 60
           M QKSLIYAFVARG V+LAEYTEFSGNFNSIA+QCLQKLPA++NKFTYNCDAHTF YL+D
Sbjct: 1   MGQKSLIYAFVARGTVILAEYTEFSGNFNSIAFQCLQKLPATSNKFTYNCDAHTFTYLLD 60

Query: 61  NGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEF---------- 110
           NGYTYCVVADES GRQ+PMAFLER++D+FV++YGG KAATAPAN LNK+F          
Sbjct: 61  NGYTYCVVADESVGRQVPMAFLERIRDDFVARYGGEKAATAPANSLNKDFSSKLKEHMQY 120

Query: 111 --------GKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQAQDFRSTG 162
                    KLAKVK QVSEVKGVMMENIEKVLDRGEKIELLVDKT NLH+QAQDFRS G
Sbjct: 121 CVDHPEEISKLAKVKDQVSEVKGVMMENIEKVLDRGEKIELLVDKTHNLHEQAQDFRSAG 180

Query: 163 TKMRRKMWLQNMKIKLIVLGILIALILIIVLSVCHGFNCGK 203
           TK+RRKMWLQNMKIKLIVLGIL+ALILIIVLSVCHGFNCGK
Sbjct: 181 TKIRRKMWLQNMKIKLIVLGILVALILIIVLSVCHGFNCGK 221

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225423678|ref|XP_002276786.1| PREDICTED: putative vesicle-associated membrane protein 726 isoform 2 [Vitis vinifera] Back     alignment and taxonomy information
>gi|427199312|gb|AFY26886.1| vesicle-associated membrane protein 72 [Morella rubra] Back     alignment and taxonomy information
>gi|356532974|ref|XP_003535044.1| PREDICTED: putative vesicle-associated membrane protein 726-like isoform 1 [Glycine max] Back     alignment and taxonomy information
>gi|351727010|ref|NP_001236634.1| uncharacterized protein LOC100500089 [Glycine max] gi|255629069|gb|ACU14879.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|255638090|gb|ACU19359.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|224115526|ref|XP_002332156.1| predicted protein [Populus trichocarpa] gi|118481984|gb|ABK92923.1| unknown [Populus trichocarpa] gi|118485253|gb|ABK94486.1| unknown [Populus trichocarpa] gi|118487184|gb|ABK95420.1| unknown [Populus trichocarpa] gi|222875206|gb|EEF12337.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356532978|ref|XP_003535046.1| PREDICTED: putative vesicle-associated membrane protein 726-like isoform 3 [Glycine max] Back     alignment and taxonomy information
>gi|255578566|ref|XP_002530145.1| Vesicle-associated membrane protein, putative [Ricinus communis] gi|223530344|gb|EEF32237.1| Vesicle-associated membrane protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|116781485|gb|ABK22119.1| unknown [Picea sitchensis] gi|116791336|gb|ABK25940.1| unknown [Picea sitchensis] 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 ?
Query203
TAIR|locus:2046595229 SAR1 "AT2G33120" [Arabidopsis 0.586 0.519 0.685 6.7e-75
TAIR|locus:2080340240 VAMP727 "AT3G54300" [Arabidops 0.458 0.387 0.655 6.9e-57
TAIR|locus:2046490217 VAMP723 "AT2G33110" [Arabidops 1.0 0.935 0.470 1.4e-46
TAIR|locus:2010627220 VAMP726 "AT1G04760" [Arabidops 0.817 0.754 0.570 2.3e-46
TAIR|locus:2010642219 VAMP721 "AT1G04750" [Arabidops 0.817 0.757 0.548 1.2e-44
TAIR|locus:2046367285 VAMP725 "AT2G32670" [Arabidops 0.817 0.582 0.542 1.2e-44
DICTYBASE|DDB_G0277173260 vamp7B "vesicle-associated mem 0.522 0.407 0.439 8.8e-32
ZFIN|ZDB-GENE-040426-1055220 sybl1 "synaptobrevin-like 1" [ 0.832 0.768 0.347 3.2e-26
RGD|621558220 Vamp7 "vesicle-associated memb 0.955 0.881 0.325 6.6e-26
MGI|MGI:1096399220 Vamp7 "vesicle-associated memb 0.980 0.904 0.321 8.4e-26
TAIR|locus:2046595 SAR1 "AT2G33120" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 449 (163.1 bits), Expect = 6.7e-75, Sum P(2) = 6.7e-75
 Identities = 87/127 (68%), Positives = 102/127 (80%)

Query:     1 MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVD 60
             M+Q+SLIY+FVARG V+L E+T+F GNF SIA QCLQKLP+SNNKFTYNCD HTFNYLV+
Sbjct:     1 MAQQSLIYSFVARGTVILVEFTDFKGNFTSIAAQCLQKLPSSNNKFTYNCDGHTFNYLVE 60

Query:    61 NGYT--------YCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGK 112
             NG++        YCVVA +S+GRQIPMAFLERVK++F  +YGGGKAATA AN LNKEFG 
Sbjct:    61 NGFSESKYCSISYCVVAVDSAGRQIPMAFLERVKEDFNKRYGGGKAATAQANSLNKEFGS 120

Query:   113 LAKVKAQ 119
               K   Q
Sbjct:   121 KLKEHMQ 127
GO:0003674 "molecular_function" evidence=ND
GO:0006810 "transport" evidence=IEA
GO:0016020 "membrane" evidence=ISS
GO:0016192 "vesicle-mediated transport" evidence=IEA
GO:0005886 "plasma membrane" evidence=IDA;TAS
GO:0005768 "endosome" evidence=IDA;TAS
GO:0005774 "vacuolar membrane" evidence=IDA
GO:0009506 "plasmodesma" evidence=IDA
GO:0009504 "cell plate" evidence=IDA
GO:0009920 "cell plate formation involved in plant-type cell wall biogenesis" evidence=IGI
GO:0072661 "protein targeting to plasma membrane" evidence=IGI
TAIR|locus:2080340 VAMP727 "AT3G54300" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2046490 VAMP723 "AT2G33110" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2010627 VAMP726 "AT1G04760" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2010642 VAMP721 "AT1G04750" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2046367 VAMP725 "AT2G32670" [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
ZFIN|ZDB-GENE-040426-1055 sybl1 "synaptobrevin-like 1" [Danio rerio (taxid:7955)] 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

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 number0.34900.95560.8818yesno
P51809VAMP7_HUMANNo assigned EC number0.34900.95560.8818yesno
Q17QI5VAMP7_BOVINNo assigned EC number0.35150.97530.9yesno
Q9ZTW3VA721_ARATHNo assigned EC number0.76250.99010.9178nono
Q9MAS5VA726_ARATHNo assigned EC number0.73970.99010.9136yesno
P47192VA722_ARATHNo assigned EC number0.75561.00.9185nono
Q5RF94VAMP7_PONABNo assigned EC number0.34900.95560.8818yesno
P70280VAMP7_MOUSENo assigned EC number0.35610.97530.9yesno

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:
GSVIVG00030156001
SubName- Full=Putative uncharacterized protein (Chromosome chr1 scaffold_5, whole genome shotgun sequence); (221 aa)
(Vitis vinifera)
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 ?
Query203
pfam0095789 pfam00957, Synaptobrevin, Synaptobrevin 2e-40
pfam1377482 pfam13774, Longin, Regulated-SNARE-like domain 2e-29
COG5143190 COG5143, SNC1, Synaptobrevin/VAMP-like protein [In 9e-12
COG5143190 COG5143, SNC1, Synaptobrevin/VAMP-like protein [In 7e-08
>gnl|CDD|201526 pfam00957, Synaptobrevin, Synaptobrevin Back     alignment and domain information 
 Score =  132 bits (335), Expect = 2e-40
 Identities = 49/86 (56%), Positives = 68/86 (79%)

Query: 112 KLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQAQDFRSTGTKMRRKMWL 171
           KL K++AQV EVK +M ENI+KVL+RGEK++LLVDKTENL   AQ FR    K++RKMW 
Sbjct: 4   KLNKIQAQVDEVKDIMTENIDKVLERGEKLDLLVDKTENLQSSAQQFRKQARKLKRKMWW 63

Query: 172 QNMKIKLIVLGILIALILIIVLSVCH 197
           +NMK+K+I+  +++ LILII++ +C 
Sbjct: 64  KNMKLKIILGLVVLILILIIIIVICG 89

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
>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 203
KOG0859217 consensus Synaptobrevin/VAMP-like protein [Intrace 100.0
KOG0862216 consensus Synaptobrevin/VAMP-like protein SEC22 [I 99.97
KOG0861198 consensus SNARE protein YKT6, synaptobrevin/VAMP s 99.95
PF0095789 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 99.95
KOG0860116 consensus Synaptobrevin/VAMP-like protein [Intrace 99.95
COG5143190 SNC1 Synaptobrevin/VAMP-like protein [Intracellula 99.83
PF1377483 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3 99.82
COG5143190 SNC1 Synaptobrevin/VAMP-like protein [Intracellula 97.57
PF0095789 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 96.86
PF0390892 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membr 96.53
KOG0811269 consensus SNARE protein PEP12/VAM3/Syntaxin 7/Synt 96.04
COG5074280 t-SNARE complex subunit, syntaxin [Intracellular t 95.01
KOG0810297 consensus SNARE protein Syntaxin 1 and related pro 94.84
KOG0781 587 consensus Signal recognition particle receptor, al 92.88
PF0390892 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membr 92.85
PF09753251 Use1: Membrane fusion protein Use1; InterPro: IPR0 92.08
PF01217141 Clat_adaptor_s: Clathrin adaptor complex small cha 91.94
PF04086279 SRP-alpha_N: Signal recognition particle, alpha su 91.63
PF1077971 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemoly 89.07
KOG0860116 consensus Synaptobrevin/VAMP-like protein [Intrace 88.74
COG5325283 t-SNARE complex subunit, syntaxin [Intracellular t 87.94
PTZ0047881 Sec superfamily; Provisional 87.19
PRK0940061 secE preprotein translocase subunit SecE; Reviewed 85.09
COG5074280 t-SNARE complex subunit, syntaxin [Intracellular t 84.3
KOG1983993 consensus Tomosyn and related SNARE-interacting pr 83.62
KOG0938 446 consensus Adaptor complexes medium subunit family 82.92
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information 
Probab=100.00  E-value=3.3e-63  Score=380.52  Aligned_cols=198  Identities=71%  Similarity=1.106  Sum_probs=191.2

Q ss_pred             cceEEEEEEeCCeEEEeecCCCCCHHHHHHHHHhcCCCC-CCeeEEEeCCeEEEEEEeCCEEEEEEecCCCCcchHHHHH
Q 028846            4 KSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFL   82 (203)
Q Consensus         4 ~~i~Ya~Iar~~~iLae~~~~~~~~~~ia~~il~ki~~~-~~k~~~~~~~~~~~~l~~~~~~~~~itd~~~~~~~af~fL   82 (203)
                      |+|+|++||||++|||||++.+|||..++.++|+|+|++ ++|++|.+|+|+|||+.+||++|+|++|++.++++||.||
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            579999999999999999999999999999999999997 6799999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCCCCCCCCCCcchHHhh-----------------HHHHHHHHHhhhhhhhhhhHHHHHHhhhhhHHHH
Q 028846           83 ERVKDEFVSKYGGGKAATAPANGLNKEFG-----------------KLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLV  145 (203)
Q Consensus        83 ~~i~~~f~~~~~~~~~~~~~~~~l~~~f~-----------------kl~~~~~~~~~v~~im~~ni~~~l~Rge~l~~l~  145 (203)
                      ++|++.|.++|+ ....++.+|++++||+                 +|++++.|++|++++|.||||++++|||+||.|+
T Consensus        81 e~Ik~~F~k~YG-~~a~ta~AysmN~EFs~vL~qqm~y~s~~p~id~lskvkaqv~evk~vM~eNIekvldRGekiELLV  159 (217)
T KOG0859|consen   81 ERIKEDFKKRYG-GGAHTAVAYSMNKEFSSVLKQQMQYCSEHPEISKLAKVKAQVTEVKGVMMENIEKVLDRGEKIELLV  159 (217)
T ss_pred             HHHHHHHHHHhc-cchhHHHHhHhHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHHHHHHHHHHHHHhccCeEEeee
Confidence            999999999996 4577788999999996                 8899999999999999999999999999999999


Q ss_pred             hhhhhhhHhHHHHHhhHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhccCCccc
Q 028846          146 DKTENLHQQAQDFRSTGTKMRRKMWLQNMKIKLIVLGILIALILIIVLSVCHGFNCG  202 (203)
Q Consensus       146 ~ks~~L~~~s~~f~~~a~~l~~~~~~~~~k~~iii~~iv~~~~~ii~~~~C~gf~C~  202 (203)
                      +||++|+.++..|++++++++|+|||+|.|+.++++++++++++||++.+||||.|-
T Consensus       160 dKTenl~~~s~~fr~q~r~~~r~mw~~n~kl~~iv~~~~~~~iyiiv~~~CgG~~~~  216 (217)
T KOG0859|consen  160 DKTENLRSKSFDFRTQGRKLRRKMWFQNMKLKLIVLGVSISLIYIIVARRCGGFTCP  216 (217)
T ss_pred             chhhhhhhhhHHHHHHHHHHHHHHHHhccceehhhhhHHHHHHHHHHHHhccCCCCC
Confidence            999999999999999999999999999999999999999999999999999999985

>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
>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
>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
>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
>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
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway 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
>COG5074 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion] 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
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [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
>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
>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
>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
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [] Back     alignment and domain information
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>COG5325 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion] Back     alignment and domain information
>PTZ00478 Sec superfamily; Provisional Back     alignment and domain information
>PRK09400 secE preprotein translocase subunit SecE; Reviewed Back     alignment and domain information
>COG5074 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion] Back     alignment and domain information
>KOG1983 consensus Tomosyn and related SNARE-interacting proteins [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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query203
4b93_A189 Complex Of Vamp7 Cytoplasmic Domain With 2nd Ankyri 1e-28
2dmw_A131 Solution Structure Of The Longin Domain Of Synaptob 3e-14
2vx8_A169 Vamp7 Longin Domain Hrb Peptide Complex Length = 16 1e-13
4afi_A173 Complex Between Vamp7 Longin Domain And Fragment Of 1e-13
2nps_A74 Crystal Structure Of The Early Endosomal Snare Comp 2e-08
3kyq_A199 Lipid-Induced Conformational Switch Controls Fusion 6e-08
2nup_C196 Crystal Structure Of The Human Sec23a24A HETERODIME 6e-08
3b5n_A61 Structure Of The Yeast Plasma Membrane Snare Comple 3e-07
2kog_A119 Lipid-Bound Synaptobrevin Solution Nmr Structure Le 4e-07
3hd7_A91 Helical Extension Of The Neuronal Snare Complex Int 5e-07
1sfc_A96 Neuronal Synaptic Fusion Complex Length = 96 7e-07
1kil_A66 Three-Dimensional Structure Of The ComplexinSNARE C 9e-07
1l4a_A80 X-Ray Structure Of The Neuronal ComplexinSNARE COMP 1e-06
1n7s_A63 High Resolution Structure Of A Truncated Neuronal S 2e-06
1gl2_A65 Crystal Structure Of An Endosomal Snare Core Comple 3e-05
3egd_C157 Crystal Structure Of The Mammalian Copii-Coat Prote 3e-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 =  122 bits (306), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 65/187 (34%), Positives = 103/187 (55%), Gaps = 18/187 (9%)
Query: 5   SLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYT 64
           ++++A VARG  +LA++    GNF  +  Q L K+P+ NNK TY+   + F+Y+  +   
Sbjct: 3   AILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIV 62
Query: 65  YCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFG------------- 111
           Y  + D+   R    +FL  VK  F + Y G +A TA    +N EF              
Sbjct: 63  YLCITDDDFERSRAFSFLNEVKKRFQTTY-GSRAQTALPYAMNSEFSSVLAAQLKHHSEN 121
Query: 112 ----KLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQAQDFRSTGTKMRR 167
               K+ + +AQV E+KG+M+ NI+ V  RGE++ELL+DKTENL   +  F++T   + R
Sbjct: 122 KSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLIDKTENLVDSSVTFKTTSRNLAR 181
Query: 168 KMWLQNM 174
            M ++N+
Sbjct: 182 AMCMKNI 188
>pdb|2DMW|A Chain A, Solution Structure Of The Longin Domain Of Synaptobrevin- Like Protein 1 Length = 131 Back     alignment and structure
>pdb|2VX8|A Chain A, Vamp7 Longin Domain Hrb Peptide Complex Length = 169 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|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|2NUP|C Chain C, Crystal Structure Of The Human Sec23a24A HETERODIMER, Complexed With The Snare Protein Sec22b Length = 196 Back     alignment and structure
>pdb|3B5N|A Chain A, Structure Of The Yeast Plasma Membrane Snare Complex Length = 61 Back     alignment and structure
>pdb|2KOG|A Chain A, Lipid-Bound Synaptobrevin Solution Nmr Structure Length = 119 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|1SFC|A Chain A, Neuronal Synaptic Fusion Complex Length = 96 Back     alignment and structure
>pdb|1KIL|A Chain A, Three-Dimensional Structure Of The ComplexinSNARE COMPLEX Length = 66 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|1N7S|A Chain A, High Resolution Structure Of A Truncated Neuronal Snare Complex Length = 63 Back     alignment and structure
>pdb|1GL2|A Chain A, Crystal Structure Of An Endosomal Snare Core Complex Length = 65 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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query203
2nut_C196 Vesicle-trafficking protein SEC22B; human copii SE 4e-41
4afi_A173 AP-3 complex subunit delta-1, vesicle-associated p 6e-41
2vx8_A169 Nucleoporin-like protein RIP, vesicle-associated m 2e-37
3kyq_A199 YKT6, synaptobrevin homolog YKT6; V-snare homolog, 6e-35
2kog_A119 Vesicle-associated membrane protein 2; synaptobrev 2e-32
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 1e-29
1l4a_A80 Synaptobrevin; snare, snare complex, membrane fusi 1e-28
2nps_A74 VAMP-4, vesicle-associated membrane protein 4; ves 2e-28
1sfc_A96 VAMP 2, protein (synaptobrevin 2); membrane fusion 1e-27
3b5n_A61 Synaptobrevin homolog 1; snare complex, syntaxin, 2e-27
1n7s_A63 Vesicle-associated membrane protein 2; neuronal sn 3e-27
1gl2_A65 Endobrevin; membrane protein, membrane fusion prot 2e-21
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-06
1urq_A63 M-tomosyn isoform; transport protein, tomosyn-snar 3e-06
>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 =  137 bits (345), Expect = 4e-41
 Identities = 44/193 (22%), Positives = 79/193 (40%), Gaps = 28/193 (14%)

Query: 7   IYAFVARGN--VVLAEYTEFSG-------NFNSIAYQCLQKLPA-SNNKFTYNCDAHTFN 56
           +   +AR    + LA   +           + S A Q  +KL   S  + T    A TF+
Sbjct: 4   LLTMIARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMTFH 63

Query: 57  YLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFG----- 111
           Y+++ G  Y V+ + +  +++  A+LE +  EF  ++G  K  T        EF      
Sbjct: 64  YIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGK-KVPTVSRPYSFIEFDTFIQK 122

Query: 112 ------------KLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQAQDFR 159
                        L  +  ++ +V+ +M+ NIE+VL RGE +  L  K  NL   ++ +R
Sbjct: 123 TKKLYIDSRARRNLGSINTELQDVQRIMVANIEEVLQRGEALSALDSKANNLSSLSKKYR 182

Query: 160 STGTKMRRKMWLQ 172
                +  +    
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
>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
>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
>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
>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
>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
>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
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 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 ?
Query203
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 99.97
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 99.97
2kog_A119 Vesicle-associated membrane protein 2; synaptobrev 99.95
2vx8_A169 Nucleoporin-like protein RIP, vesicle-associated m 99.94
1sfc_A96 VAMP 2, protein (synaptobrevin 2); membrane fusion 99.88
2nps_A74 VAMP-4, vesicle-associated membrane protein 4; ves 99.87
1l4a_A80 Synaptobrevin; snare, snare complex, membrane fusi 99.86
3bw6_A144 Synaptobrevin homolog YKT6; YKT6P, farnesylation, 99.84
3b5n_A61 Synaptobrevin homolog 1; snare complex, syntaxin, 99.81
1n7s_A63 Vesicle-associated membrane protein 2; neuronal sn 99.79
1gl2_A65 Endobrevin; membrane protein, membrane fusion prot 99.7
1urq_A63 M-tomosyn isoform; transport protein, tomosyn-snar 99.63
3fie_C38 Fragment of vesicle-associated membrane protein 2; 98.04
3zym_A310 Phosphatidylinositol-binding clathrin assembly PR 97.68
2fh5_A185 Signal recognition particle receptor alpha subunit 97.39
3hd7_B109 Syntaxin-1A; membrane protein, coiled-coil, 4-heli 97.32
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 94.86
2vgl_S142 AP-2 complex subunit sigma-1; cytoplasmic vesicle, 94.37
1w63_Q158 Adapter-related protein complex 1 sigma 1A subunit 94.16
3tjz_C153 Coatomer subunit zeta-1; protein trafficking, golg 92.17
3hd7_B109 Syntaxin-1A; membrane protein, coiled-coil, 4-heli 91.46
1w63_M 423 Adaptor-related protein complex 1, MU 1 subunit; e 89.75
2vgl_M 435 AP-2 complex subunit MU-1; cytoplasmic vesicle, al 89.28
2kog_A119 Vesicle-associated membrane protein 2; synaptobrev 85.78
1jth_B77 Syntaxin 1A; coiled-coil, polar layer, endocytosis 81.86
2fz0_A149 R-snare NYV1P, V-snare component of the vacuolar s 81.08
1rh5_B74 Preprotein translocase SECE subunit; protein trans 80.57
>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=1.1e-53  Score=336.92  Aligned_cols=172  Identities=38%  Similarity=0.664  Sum_probs=135.3

Q ss_pred             CcceEEEEEEeCCeEEEeecCCCCCHHHHHHHHHhcCCCCCCeeEEEeCCeEEEEEEeCCEEEEEEecCCCCcchHHHHH
Q 028846            3 QKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFL   82 (203)
Q Consensus         3 ~~~i~Ya~Iar~~~iLae~~~~~~~~~~ia~~il~ki~~~~~k~~~~~~~~~~~~l~~~~~~~~~itd~~~~~~~af~fL   82 (203)
                      .|+|+|||||||++|||||+..+|||..+++++|+++|+.+++.++++|+|.|||+.++|++|+|+||++||+++||.||
T Consensus         1 ~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            1 SMAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIVYLCITDDDFERSRAFSFL   80 (189)
T ss_dssp             CCSEEEEEEEETTEEEEEEESSEECHHHHHHHHHTTCCSSSEEEEEEETTEEEEEEEETTEEEEEEEETTSCHHHHHHHH
T ss_pred             CCceEEEEEEeCCEEEEeCCCCCCCHHHHHHHHHHhCCCCCCeEEEEECCEEEEEEEeCCeEEEEEEcCccCHHHHHHHH
Confidence            47899999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCCCCCCCCCCcchHHhh-----------------HHHHHHHHHhhhhhhhhhhHHHHHHhhhhhHHHH
Q 028846           83 ERVKDEFVSKYGGGKAATAPANGLNKEFG-----------------KLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLV  145 (203)
Q Consensus        83 ~~i~~~f~~~~~~~~~~~~~~~~l~~~f~-----------------kl~~~~~~~~~v~~im~~ni~~~l~Rge~l~~l~  145 (203)
                      ++|+++|.+.|+ ..+.++.|++++.+|+                 ++.+++++++||++||.+||+++|+|||+||.|+
T Consensus        81 ~~i~~eF~~~~~-~~~~~~~~~~~~~~f~~~l~~~~~~y~d~~~~d~l~~~~~~l~ev~~im~~Ni~~vl~Rge~l~~L~  159 (189)
T 4b93_A           81 NEVKKRFQTTYG-SRAQTALPYAMNSEFSSVLAAQLKHHSENKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLI  159 (189)
T ss_dssp             HHHHHHHHHHHG-GGGGTCCTTTTHHHHHHHHHHHHHHHHCC-------CCHHHHHTTTTCCEECCCCBCTTSSBCCCCE
T ss_pred             HHHHHHHHhhcc-ccccccCCccccchhhHHHHHHHHhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Confidence            999999999995 4556667777766664                 7888999999999999999999999999999999


Q ss_pred             hhhhhhhHhHHHHHhhHHHHHHHHHHHhhH
Q 028846          146 DKTENLHQQAQDFRSTGTKMRRKMWLQNMK  175 (203)
Q Consensus       146 ~ks~~L~~~s~~f~~~a~~l~~~~~~~~~k  175 (203)
                      +||++|+.+|..|+++|++++|+|||+|+|
T Consensus       160 ~ks~~L~~~s~~f~~~a~~l~r~mwwkn~K  189 (189)
T 4b93_A          160 DKTENLVDSSVTFKTTSRNLARAMCMKNIK  189 (189)
T ss_dssp             ETTCC-------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            999999999999999999999999999987
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2kog_A Vesicle-associated membrane protein 2; synaptobrevin, VAMP2, DPC micelle, snare, coiled coil, membrane fusion, transmembrane; NMR {Rattus norvegicus} 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
>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
>1rh5_B Preprotein translocase SECE subunit; protein translocation, SECY, membrane protein, protein channels, protein transport; 3.20A {Methanocaldococcus jannaschii} SCOP: f.23.28.1 PDB: 1rhz_B 2yxq_B 2yxr_B 3dkn_B 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 203
d1ifqa_127 d.110.4.1 (A:) Sec22b {Mouse (Mus musculus) [TaxId 2e-24
d1ioua_140 d.110.4.1 (A:) Synaptobrevin homolog 1 ykt6 {Baker 1e-10
d2fh5a1129 d.110.4.4 (A:1-129) Signal recognition particle re 0.001
>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 = 91.0 bits (226), Expect = 2e-24
 Identities = 25/101 (24%), Positives = 46/101 (45%), Gaps = 10/101 (9%)

Query: 5   SLIYAFVARGN--VVLAEYTEFSGNFN-------SIAYQCLQKLPA-SNNKFTYNCDAHT 54
           S++   +AR    + LA   +             S A Q  +KL   S  + T    A T
Sbjct: 1   SVLLTMIARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMT 60

Query: 55  FNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGG 95
           F+Y+++ G  Y V+ + +  +++  A+LE +  EF  ++G 
Sbjct: 61  FHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGK 101
>d1ioua_ d.110.4.1 (A:) Synaptobrevin homolog 1 ykt6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 140 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]} Length = 129 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 ?
Query203
d1ifqa_127 Sec22b {Mouse (Mus musculus) [TaxId: 10090]} 99.91
d1ioua_140 Synaptobrevin homolog 1 ykt6 {Baker's yeast (Sacch 99.55
d2fh5a1129 Signal recognition particle receptor alpha subunit 97.89
d2vgls_142 Sigma2 adaptin (clathrin coat assembly protein AP1 96.33
d2vglm2141 Mu2 adaptin (clathrin coat assembly protein AP50) 95.41
>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=99.91  E-value=9.7e-24  Score=153.75  Aligned_cols=113  Identities=27%  Similarity=0.432  Sum_probs=95.3

Q ss_pred             ceEEEEEEeC--CeEEEeecCCCCC-------HHHHHHHHHhcCCCC-CCeeEEEeCCeEEEEEEeCCEEEEEEecCCCC
Q 028846            5 SLIYAFVARG--NVVLAEYTEFSGN-------FNSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDNGYTYCVVADESSG   74 (203)
Q Consensus         5 ~i~Ya~Iar~--~~iLae~~~~~~~-------~~~ia~~il~ki~~~-~~k~~~~~~~~~~~~l~~~~~~~~~itd~~~~   74 (203)
                      .|+|++|||+  +.||+|+++.+++       +...|+.++++++|+ +++.+++.++|.|||++++|++|+|+||++||
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            4899999996  4799999876653       235788999999876 68999999999999999999999999999999


Q ss_pred             cchHHHHHHHHHHHHHhhcCCCCCCC-CCCCcchHHhh-HHHHHHHH
Q 028846           75 RQIPMAFLERVKDEFVSKYGGGKAAT-APANGLNKEFG-KLAKVKAQ  119 (203)
Q Consensus        75 ~~~af~fL~~i~~~f~~~~~~~~~~~-~~~~~l~~~f~-kl~~~~~~  119 (203)
                      +++||.||++|+++|.+.|+ +.+.+ ..||+| -+|+ -|.+++++
T Consensus        81 ~~laF~fLeei~~eF~~~y~-~~i~~~~rpy~F-i~Fd~~iqk~k~~  125 (127)
T d1ifqa_          81 KKLAFAYLEDLHSEFDEQHG-KKVPTVSRPYSF-IEFDTFIQKTKKL  125 (127)
T ss_dssp             HHHHHHHHHHHHHHHHHHHT-TTTTTCCSTTTT-GGGHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhhh-hhhhcccCCcch-HHHHHHHHHHHHh
Confidence            99999999999999999995 45554 458999 5898 45555543
>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