Citrus Sinensis ID: 027768

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-------210-------22
MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRQQGTKMRRKMWIQNMKIKLIVLGIIIALILIIVLSVCHGFKC
cccccEEEEEEEEccEEEEEEccccccHHHHHHHHHccccccccEEEEEEccEEEEEEEEccEEEEEEEccccccccHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
ccccHEEEEEEEcccEEEEEEccccccHHHHHHHHHHHcccccccEEEEcccEEEEEEEcccEEEEEEEccHcccccHHHHHHHHHHHHHHHHccccHccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLqklpatnnkftyncdghtfnylVENGFTYCVVAVESAGRQIPIAFLERVKEDFnkrygggkaATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRQQGTKMRRKMWIQNMKIKLIVLGIIIALILIIVLSVCHGFKC
MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVdktenlrsqaqdfrqqgtkmrRKMWIQNMKIKLIVLGIIIALILIIVLSVCHGFKC
MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRQQGTKMRRKMWIQNMkiklivlgiiialiliivlSVCHGFKC
*****LIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVD*******************RRKMWIQNMKIKLIVLGIIIALILIIVLSVCHGF**
**QQSLIYSFVARGTVILAEYTEFTGNFTSIAS*C************YNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEH***********************VKGVMMENIEKVLDRGEKI*********************TKMRRKMWIQNMKIKLIVLGIIIALILIIVLSVCHGFKC
MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQA*********MRRKMWIQNMKIKLIVLGIIIALILIIVLSVCHGFKC
**QQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRQQGTKMRRKMWIQNMKIKLIVLGIIIALILIIVLSVCHGFKC
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MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKxxxxxxxxxxxxxxxxxxxxxGTKMRRKMWIQNMKIKLIVLGIIIALILIIVLSVCHGFKC
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 ?
Query219 2.2.26 [Sep-21-2011]
Q9MAS5220 Putative vesicle-associat yes no 1.0 0.995 0.894 1e-111
Q9ZTW3219 Vesicle-associated membra no no 1.0 1.0 0.908 1e-108
O48850285 Vesicle-associated membra no no 1.0 0.768 0.899 1e-107
P47192221 Vesicle-associated membra no no 1.0 0.990 0.904 1e-106
O23429222 Vesicle-associated membra no no 1.0 0.986 0.727 5e-88
Q8VY69217 Vesicle-associated membra no no 0.981 0.990 0.744 1e-81
Q9M376240 Vesicle-associated membra no no 1.0 0.912 0.584 3e-81
Q9LFP1221 Vesicle-associated membra no no 0.954 0.945 0.4 1e-41
Q9FMR5221 Vesicle-associated membra no no 0.958 0.950 0.359 1e-39
O49377219 Vesicle-associated membra no no 0.958 0.958 0.384 6e-39
>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 =  402 bits (1032), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 196/219 (89%), Positives = 211/219 (96%)

Query: 1   MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVE 60
           MGQQSLIYSFVARGTVILAEYTEF GNFTS+A+QCLQKLP++NNKFTYNCDGHTFNYL +
Sbjct: 1   MGQQSLIYSFVARGTVILAEYTEFKGNFTSVAAQCLQKLPSSNNKFTYNCDGHTFNYLAD 60

Query: 61  NGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQY 120
           NGFTYCVV +ESAGRQIP+AFLERVKEDFNKRYGGGKA+TA ANSLNKEFGSKLKEHMQY
Sbjct: 61  NGFTYCVVVIESAGRQIPMAFLERVKEDFNKRYGGGKASTAKANSLNKEFGSKLKEHMQY 120

Query: 121 CVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRQQG 180
           C DHPEEISKL+KVKAQV+EVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFR QG
Sbjct: 121 CADHPEEISKLSKVKAQVTEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRTQG 180

Query: 181 TKMRRKMWIQNMKIKLIVLGIIIALILIIVLSVCHGFKC 219
           TKM+RK+W +NMKIKLIV GII+ALILII+LSVCHGFKC
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|O48850|VA725_ARATH Vesicle-associated membrane protein 725 OS=Arabidopsis thaliana GN=VAMP725 PE=2 SV=2 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|O23429|VA724_ARATH Vesicle-associated membrane protein 724 OS=Arabidopsis thaliana GN=VAMP724 PE=2 SV=2 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|Q9M376|VA727_ARATH Vesicle-associated membrane protein 727 OS=Arabidopsis thaliana GN=VAMP727 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 ?
Query219
449432442219 PREDICTED: putative vesicle-associated m 1.0 1.0 0.945 1e-113
255554170219 Vesicle-associated membrane protein, put 1.0 1.0 0.977 1e-113
116781485222 unknown [Picea sitchensis] gi|116791336| 1.0 0.986 0.867 1e-112
224075615219 predicted protein [Populus trichocarpa] 1.0 1.0 0.963 1e-112
225462779220 PREDICTED: putative vesicle-associated m 1.0 0.995 0.963 1e-111
192910812220 synaptobrevin 1 [Elaeis guineensis] 1.0 0.995 0.940 1e-110
356577544221 PREDICTED: putative vesicle-associated m 1.0 0.990 0.831 1e-110
15220315220 vesicle-associated membrane protein 72 [ 1.0 0.995 0.894 1e-110
297843284220 vesicle-associated membrane protein 7B [ 1.0 0.995 0.894 1e-109
356533328221 PREDICTED: putative vesicle-associated m 1.0 0.990 0.826 1e-108
>gi|449432442|ref|XP_004134008.1| PREDICTED: putative vesicle-associated membrane protein 726-like [Cucumis sativus] gi|449487534|ref|XP_004157674.1| PREDICTED: putative vesicle-associated membrane protein 726-like [Cucumis sativus] Back     alignment and taxonomy information
 Score =  412 bits (1060), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 207/219 (94%), Positives = 217/219 (99%)

Query: 1   MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVE 60
           MGQQ+LIYSFVARGTVILAEYTEFTGNFT+IASQCLQKLPA+NNKFTYNCDGHTFNYLVE
Sbjct: 1   MGQQTLIYSFVARGTVILAEYTEFTGNFTTIASQCLQKLPASNNKFTYNCDGHTFNYLVE 60

Query: 61  NGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQY 120
           NGFTYCVVA+E+AGRQIPIAFLERVKEDFNKRYGGGKAATAVA+SLNKEFGSKLKEHMQY
Sbjct: 61  NGFTYCVVAIEAAGRQIPIAFLERVKEDFNKRYGGGKAATAVAHSLNKEFGSKLKEHMQY 120

Query: 121 CVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRQQG 180
           C+DHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFR QG
Sbjct: 121 CLDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRTQG 180

Query: 181 TKMRRKMWIQNMKIKLIVLGIIIALILIIVLSVCHGFKC 219
           TKMRRKMW QNMKIKLIVLGII+ALILII+LSVCHGF+C
Sbjct: 181 TKMRRKMWFQNMKIKLIVLGIIVALILIIILSVCHGFQC 219

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255554170|ref|XP_002518125.1| Vesicle-associated membrane protein, putative [Ricinus communis] gi|223542721|gb|EEF44258.1| 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
>gi|224075615|ref|XP_002304708.1| predicted protein [Populus trichocarpa] gi|222842140|gb|EEE79687.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225462779|ref|XP_002264270.1| PREDICTED: putative vesicle-associated membrane protein 726 [Vitis vinifera] gi|296090506|emb|CBI40837.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|192910812|gb|ACF06514.1| synaptobrevin 1 [Elaeis guineensis] Back     alignment and taxonomy information
>gi|356577544|ref|XP_003556884.1| PREDICTED: putative vesicle-associated membrane protein 726-like [Glycine max] Back     alignment and taxonomy information
>gi|15220315|ref|NP_171968.1| vesicle-associated membrane protein 72 [Arabidopsis thaliana] gi|83288285|sp|Q9MAS5.2|VA726_ARATH RecName: Full=Putative vesicle-associated membrane protein 726; Short=AtVAMP726 gi|332189619|gb|AEE27740.1| vesicle-associated membrane protein 72 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297843284|ref|XP_002889523.1| vesicle-associated membrane protein 7B [Arabidopsis lyrata subsp. lyrata] gi|297335365|gb|EFH65782.1| vesicle-associated membrane protein 7B [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|356533328|ref|XP_003535217.1| PREDICTED: putative vesicle-associated membrane protein 726-like [Glycine max] 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 ?
Query219
TAIR|locus:2010627220 VAMP726 "AT1G04760" [Arabidops 1.0 0.995 0.821 5.9e-96
TAIR|locus:2010642219 VAMP721 "AT1G04750" [Arabidops 1.0 1.0 0.826 2.6e-95
TAIR|locus:2046367285 VAMP725 "AT2G32670" [Arabidops 1.0 0.768 0.821 6.8e-95
TAIR|locus:2046595229 SAR1 "AT2G33120" [Arabidopsis 1.0 0.956 0.792 5e-92
TAIR|locus:2046490217 VAMP723 "AT2G33110" [Arabidops 0.981 0.990 0.671 2e-72
TAIR|locus:2080340240 VAMP727 "AT3G54300" [Arabidops 0.543 0.495 0.579 1.6e-69
TAIR|locus:2116672219 VAMP711 "vesicle-associated me 0.958 0.958 0.366 1.9e-35
TAIR|locus:2147952221 VAMP713 "AT5G11150" [Arabidops 0.958 0.950 0.373 4e-35
TAIR|locus:2176342221 VAMP714 "AT5G22360" [Arabidops 0.844 0.837 0.370 6.7e-33
DICTYBASE|DDB_G0277173260 vamp7B "vesicle-associated mem 0.963 0.811 0.336 1.3e-31
TAIR|locus:2010627 VAMP726 "AT1G04760" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 954 (340.9 bits), Expect = 5.9e-96, P = 5.9e-96
 Identities = 180/219 (82%), Positives = 193/219 (88%)

Query:     1 MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVE 60
             MGQQSLIYSFVARGTVILAEYTEF GNFTS+A+QCLQKLP++NNKFTYNCDGHTFNYL +
Sbjct:     1 MGQQSLIYSFVARGTVILAEYTEFKGNFTSVAAQCLQKLPSSNNKFTYNCDGHTFNYLAD 60

Query:    61 NGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQY 120
             NGFTYCVV +ESAGRQIP+AFLERVKEDFNKRYGGGKA+TA ANSLNKEFGSKLKEHMQY
Sbjct:    61 NGFTYCVVVIESAGRQIPMAFLERVKEDFNKRYGGGKASTAKANSLNKEFGSKLKEHMQY 120

Query:   121 CVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRQQG 180
             C DHPEEISKL+KVKAQV+EVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFR QG
Sbjct:   121 CADHPEEISKLSKVKAQVTEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRTQG 180

Query:   181 TKMRRKMWIQNMXXXXXXXXXXXXXXXXXXXSVCHGFKC 219
             TKM+RK+W +NM                   SVCHGFKC
Sbjct:   181 TKMKRKLWFENMKIKLIVFGIIVALILIIILSVCHGFKC 219
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:0009507 "chloroplast" evidence=IDA
GO:0005768 "endosome" evidence=TAS
GO:0005886 "plasma membrane" evidence=TAS
GO:0048451 "petal formation" evidence=RCA
GO:0048453 "sepal formation" evidence=RCA
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
TAIR|locus:2046595 SAR1 "AT2G33120" [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:2080340 VAMP727 "AT3G54300" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2116672 VAMP711 "vesicle-associated membrane protein 711" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2147952 VAMP713 "AT5G11150" [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

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 number0.35210.96340.9590yesno
P51809VAMP7_HUMANNo assigned EC number0.35810.95430.95yesno
Q17QI5VAMP7_BOVINNo assigned EC number0.35810.95430.95yesno
O23429VA724_ARATHNo assigned EC number0.72721.00.9864nono
Q9ZTW3VA721_ARATHNo assigned EC number0.90861.01.0nono
Q8VY69VA723_ARATHNo assigned EC number0.74420.98170.9907nono
Q9MAS5VA726_ARATHNo assigned EC number0.89491.00.9954yesno
Q5ZL74VAMP7_CHICKNo assigned EC number0.36450.84930.8454yesno
P47192VA722_ARATHNo assigned EC number0.90411.00.9909nono
Q86AQ7VAM7B_DICDINo assigned EC number0.36910.96340.8115yesno
Q5RF94VAMP7_PONABNo assigned EC number0.35810.95430.95yesno
P70280VAMP7_MOUSENo assigned EC number0.35930.84930.8454yesno

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

Fail to connect to STRING server

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 ?
Query219
pfam0095789 pfam00957, Synaptobrevin, Synaptobrevin 1e-40
pfam1377482 pfam13774, Longin, Regulated-SNARE-like domain 3e-27
COG5143190 COG5143, SNC1, Synaptobrevin/VAMP-like protein [In 9e-13
COG5143190 COG5143, SNC1, Synaptobrevin/VAMP-like protein [In 1e-07
>gnl|CDD|201526 pfam00957, Synaptobrevin, Synaptobrevin Back     alignment and domain information 
 Score =  133 bits (337), Expect = 1e-40
 Identities = 51/89 (57%), Positives = 72/89 (80%)

Query: 127 EISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRQQGTKMRRK 186
              KL K++AQV EVK +M ENI+KVL+RGEK++LLVDKTENL+S AQ FR+Q  K++RK
Sbjct: 1   SNDKLNKIQAQVDEVKDIMTENIDKVLERGEKLDLLVDKTENLQSSAQQFRKQARKLKRK 60

Query: 187 MWIQNMKIKLIVLGIIIALILIIVLSVCH 215
           MW +NMK+K+I+  +++ LILII++ +C 
Sbjct: 61  MWWKNMKLKIILGLVVLILILIIIIVICG 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 219
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
PF0095789 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 99.96
COG5143190 SNC1 Synaptobrevin/VAMP-like protein [Intracellula 99.91
PF1377483 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3 99.8
COG5143190 SNC1 Synaptobrevin/VAMP-like protein [Intracellula 97.95
PF0095789 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 96.91
PF0390892 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membr 96.86
KOG0811269 consensus SNARE protein PEP12/VAM3/Syntaxin 7/Synt 96.68
KOG0810297 consensus SNARE protein Syntaxin 1 and related pro 96.38
COG5074280 t-SNARE complex subunit, syntaxin [Intracellular t 95.99
PF04086279 SRP-alpha_N: Signal recognition particle, alpha su 94.79
PF0390892 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membr 94.64
PF09753251 Use1: Membrane fusion protein Use1; InterPro: IPR0 93.24
KOG0781 587 consensus Signal recognition particle receptor, al 93.03
KOG0860116 consensus Synaptobrevin/VAMP-like protein [Intrace 91.34
PRK0102677 tetrahydromethanopterin S-methyltransferase subuni 89.61
PF04099142 Sybindin: Sybindin-like family ; InterPro: IPR0072 89.49
COG5074280 t-SNARE complex subunit, syntaxin [Intracellular t 88.62
TIGR0114970 mtrG N5-methyltetrahydromethanopterin:coenzyme M m 88.47
PF0421070 MtrG: Tetrahydromethanopterin S-methyltransferase, 88.08
PF1077971 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemoly 86.83
KOG1983993 consensus Tomosyn and related SNARE-interacting pr 86.83
PF09426141 Nyv1_N: Vacuolar R-SNARE Nyv1 N terminal; InterPro 86.44
PF01217141 Clat_adaptor_s: Clathrin adaptor complex small cha 85.26
PTZ0047881 Sec superfamily; Provisional 84.94
COG5325283 t-SNARE complex subunit, syntaxin [Intracellular t 84.19
KOG3385118 consensus V-SNARE [Intracellular trafficking, secr 83.68
PF04799171 Fzo_mitofusin: fzo-like conserved region; InterPro 83.34
PF06789159 UPF0258: Uncharacterised protein family (UPF0258); 82.77
PRK0940061 secE preprotein translocase subunit SecE; Reviewed 82.13
PF03904230 DUF334: Domain of unknown function (DUF334); Inter 81.85
PF1116698 DUF2951: Protein of unknown function (DUF2951); In 80.87
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information 
Probab=100.00  E-value=1.6e-69  Score=413.19  Aligned_cols=214  Identities=77%  Similarity=1.173  Sum_probs=208.3

Q ss_pred             cceEEEEEEeCCeEEEeecCCCCCHHHHHHHHhccCCCC-CCeeEEEECCeEEEEEeeCCEEEEEEecCCcccchHHHHH
Q 027768            4 QSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPAT-NNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFL   82 (219)
Q Consensus         4 ~~i~Ya~Iar~~~iLae~~~~~~~~~~ia~~il~ki~~~-~~k~~~~~~~~~~~~l~~~~~~~~~vtd~~~~~~~af~fL   82 (219)
                      |+|+|+.||||++|||||++.+|||..++.++|+|+|++ ++|++|++|+|+|||+.+||++|+|++|++.++++||.||
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            689999999999999999999999999999999999998 5699999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhcCCCCccccccccchHHHhHHHHHhchhhcCCchhhhHHHHHHHHHHhHHHHHHHhHHHHHhhhHHHHHH
Q 027768           83 ERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELL  162 (219)
Q Consensus        83 ~~i~~~f~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~~dkl~~i~~~l~~vk~im~~Ni~~vl~Rge~L~~l  162 (219)
                      ++|++.|.+.|+ ...+++.+|+++++|++.|++.|++|.++|+ .|++.+++.+++|||++|.+|||++++|||+||.|
T Consensus        81 e~Ik~~F~k~YG-~~a~ta~AysmN~EFs~vL~qqm~y~s~~p~-id~lskvkaqv~evk~vM~eNIekvldRGekiELL  158 (217)
T KOG0859|consen   81 ERIKEDFKKRYG-GGAHTAVAYSMNKEFSSVLKQQMQYCSEHPE-ISKLAKVKAQVTEVKGVMMENIEKVLDRGEKIELL  158 (217)
T ss_pred             HHHHHHHHHHhc-cchhHHHHhHhHHHHHHHHHHHHHHHHcCcc-hhHHHHHHHHHHHHHHHHHHHHHHHHhccCeEEee
Confidence            999999999996 4578889999999999999999999999998 69999999999999999999999999999999999


Q ss_pred             HHHhhhHHHHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 027768          163 VDKTENLRSQAQDFRQQGTKMRRKMWIQNMKIKLIVLGIIIALILIIVLSVCHGFKC  219 (219)
Q Consensus       163 ~~ks~~L~~~s~~f~~~a~~l~~~~~~~~~k~~~ii~~vv~~~~~~i~~~~C~gf~c  219 (219)
                      ++||++|+.+|..|++++++++|+|||+|.|+++++++++++++++|++.+||||.|
T Consensus       159 VdKTenl~~~s~~fr~q~r~~~r~mw~~n~kl~~iv~~~~~~~iyiiv~~~CgG~~~  215 (217)
T KOG0859|consen  159 VDKTENLRSKSFDFRTQGRKLRRKMWFQNMKLKLIVLGVSISLIYIIVARRCGGFTC  215 (217)
T ss_pred             echhhhhhhhhHHHHHHHHHHHHHHHHhccceehhhhhHHHHHHHHHHHHhccCCCC
Confidence            999999999999999999999999999999999999999999999999999999987

>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
>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
>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
>KOG0810 consensus SNARE protein Syntaxin 1 and related proteins [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
>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
>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
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [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
>PRK01026 tetrahydromethanopterin S-methyltransferase subunit G; Provisional 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
>COG5074 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion] Back     alignment and domain information
>TIGR01149 mtrG N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit G Back     alignment and domain information
>PF04210 MtrG: Tetrahydromethanopterin S-methyltransferase, subunit G ; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea 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
>KOG1983 consensus Tomosyn and related SNARE-interacting proteins [Intracellular trafficking, secretion, and vesicular transport] 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
>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
>PTZ00478 Sec superfamily; Provisional Back     alignment and domain information
>COG5325 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion] Back     alignment and domain information
>KOG3385 consensus V-SNARE [Intracellular trafficking, secretion, and vesicular 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
>PF06789 UPF0258: Uncharacterised protein family (UPF0258); InterPro: IPR009626 This is a group of proteins of unknown function Back     alignment and domain information
>PRK09400 secE preprotein translocase subunit SecE; Reviewed Back     alignment and domain information
>PF03904 DUF334: Domain of unknown function (DUF334); InterPro: IPR005602 This is a family of proteins found in Staphylococcus aureus plasmid with no characterised function Back     alignment and domain information
>PF11166 DUF2951: Protein of unknown function (DUF2951); InterPro: IPR021337 This family of proteins has no known function 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 ?
Query219
4b93_A189 Complex Of Vamp7 Cytoplasmic Domain With 2nd Ankyri 7e-31
4afi_A173 Complex Between Vamp7 Longin Domain And Fragment Of 3e-15
2vx8_A169 Vamp7 Longin Domain Hrb Peptide Complex Length = 16 7e-15
2dmw_A131 Solution Structure Of The Longin Domain Of Synaptob 3e-14
2nup_C196 Crystal Structure Of The Human Sec23a24A HETERODIME 4e-10
2nps_A74 Crystal Structure Of The Early Endosomal Snare Comp 2e-08
3b5n_A61 Structure Of The Yeast Plasma Membrane Snare Comple 5e-08
3kyq_A199 Lipid-Induced Conformational Switch Controls Fusion 8e-07
1kil_A66 Three-Dimensional Structure Of The ComplexinSNARE C 9e-07
2kog_A119 Lipid-Bound Synaptobrevin Solution Nmr Structure Le 1e-06
3hd7_A91 Helical Extension Of The Neuronal Snare Complex Int 1e-06
1sfc_A96 Neuronal Synaptic Fusion Complex Length = 96 2e-06
1n7s_A63 High Resolution Structure Of A Truncated Neuronal S 4e-06
1l4a_A80 X-Ray Structure Of The Neuronal ComplexinSNARE COMP 4e-06
3egd_C157 Crystal Structure Of The Mammalian Copii-Coat Prote 4e-05
1gl2_A65 Crystal Structure Of An Endosomal Snare Core Comple 2e-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 =  130 bits (326), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 68/190 (35%), Positives = 112/190 (58%), Gaps = 6/190 (3%)
Query: 5   SLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFT 64
           +++++ VARGT ILA++    GNF  +  Q L K+P+ NNK TY+   + F+Y+ ++   
Sbjct: 3   AILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIV 62
Query: 65  YCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDH 124
           Y  +  +   R    +FL  VK+ F   Y G +A TA+  ++N EF S L   +++   H
Sbjct: 63  YLCITDDDFERSRAFSFLNEVKKRFQTTY-GSRAQTALPYAMNSEFSSVLAAQLKH---H 118
Query: 125 PE--EISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQAQDFRQQGTK 182
            E   + K+ + +AQV E+KG+M+ NI+ V  RGE++ELL+DKTENL   +  F+     
Sbjct: 119 SENKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLIDKTENLVDSSVTFKTTSRN 178
Query: 183 MRRKMWIQNM 192
           + R M ++N+
Sbjct: 179 LARAMCMKNI 188
>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|2DMW|A Chain A, Solution Structure Of The Longin Domain Of Synaptobrevin- Like Protein 1 Length = 131 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|3B5N|A Chain A, Structure Of The Yeast Plasma Membrane Snare Complex Length = 61 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|1KIL|A Chain A, Three-Dimensional Structure Of The ComplexinSNARE COMPLEX Length = 66 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|1N7S|A Chain A, High Resolution Structure Of A Truncated Neuronal Snare Complex Length = 63 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|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|1GL2|A Chain A, Crystal Structure Of An Endosomal Snare Core Complex Length = 65 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 ?
Query219
4afi_A173 AP-3 complex subunit delta-1, vesicle-associated p 1e-47
2nut_C196 Vesicle-trafficking protein SEC22B; human copii SE 9e-47
2vx8_A169 Nucleoporin-like protein RIP, vesicle-associated m 1e-44
3kyq_A199 YKT6, synaptobrevin homolog YKT6; V-snare homolog, 5e-39
2kog_A119 Vesicle-associated membrane protein 2; synaptobrev 8e-33
1l4a_A80 Synaptobrevin; snare, snare complex, membrane fusi 2e-30
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 1e-29
2nps_A74 VAMP-4, vesicle-associated membrane protein 4; ves 2e-28
3b5n_A61 Synaptobrevin homolog 1; snare complex, syntaxin, 4e-28
1sfc_A96 VAMP 2, protein (synaptobrevin 2); membrane fusion 6e-28
1n7s_A63 Vesicle-associated membrane protein 2; neuronal sn 1e-27
1gl2_A65 Endobrevin; membrane protein, membrane fusion prot 7e-22
1urq_A63 M-tomosyn isoform; transport protein, tomosyn-snar 9e-06
>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
 Score =  153 bits (388), Expect = 1e-47
 Identities = 39/124 (31%), Positives = 68/124 (54%), Gaps = 1/124 (0%)

Query: 1   MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVE 60
               +++++ VARGT ILA++    GNF  +  Q L K+P+ NNK TY+   + F+Y+ +
Sbjct: 51  EEAMAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQ 110

Query: 61  NGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQY 120
           +   Y  +  +   R    +FL  VK+ F   Y G +A TA+  ++N EF S L   +++
Sbjct: 111 DRIVYLCITDDDFERSRAFSFLNEVKKRFQTTY-GSRAQTALPYAMNSEFSSVLAAQLKH 169

Query: 121 CVDH 124
             ++
Sbjct: 170 HSEN 173
>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
>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
>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
>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
>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
>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
>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
>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 ?
Query219
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
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 99.98
2vx8_A169 Nucleoporin-like protein RIP, vesicle-associated m 99.96
2kog_A119 Vesicle-associated membrane protein 2; synaptobrev 99.96
2nps_A74 VAMP-4, vesicle-associated membrane protein 4; ves 99.92
3bw6_A144 Synaptobrevin homolog YKT6; YKT6P, farnesylation, 99.91
1sfc_A96 VAMP 2, protein (synaptobrevin 2); membrane fusion 99.91
1l4a_A80 Synaptobrevin; snare, snare complex, membrane fusi 99.9
3b5n_A61 Synaptobrevin homolog 1; snare complex, syntaxin, 99.86
1n7s_A63 Vesicle-associated membrane protein 2; neuronal sn 99.86
1gl2_A65 Endobrevin; membrane protein, membrane fusion prot 99.8
1urq_A63 M-tomosyn isoform; transport protein, tomosyn-snar 99.71
3zym_A310 Phosphatidylinositol-binding clathrin assembly PR 98.29
3fie_C38 Fragment of vesicle-associated membrane protein 2; 98.2
3hd7_B109 Syntaxin-1A; membrane protein, coiled-coil, 4-heli 97.78
2fh5_A185 Signal recognition particle receptor alpha subunit 97.54
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 95.02
1w63_Q158 Adapter-related protein complex 1 sigma 1A subunit 90.93
2vgl_S142 AP-2 complex subunit sigma-1; cytoplasmic vesicle, 89.42
2fz0_A149 R-snare NYV1P, V-snare component of the vacuolar s 88.52
3hd7_B109 Syntaxin-1A; membrane protein, coiled-coil, 4-heli 88.21
1jth_B77 Syntaxin 1A; coiled-coil, polar layer, endocytosis 88.17
2kog_A119 Vesicle-associated membrane protein 2; synaptobrev 87.83
1w63_M 423 Adaptor-related protein complex 1, MU 1 subunit; e 86.99
2vgl_M 435 AP-2 complex subunit MU-1; cytoplasmic vesicle, al 82.07
1n7s_A63 Vesicle-associated membrane protein 2; neuronal sn 80.95
>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=2e-59  Score=369.99  Aligned_cols=189  Identities=35%  Similarity=0.622  Sum_probs=149.7

Q ss_pred             CcceEEEEEEeCCeEEEeecCCCCCHHHHHHHHhccCCCCCCeeEEEECCeEEEEEeeCCEEEEEEecCCcccchHHHHH
Q 027768            3 QQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFL   82 (219)
Q Consensus         3 ~~~i~Ya~Iar~~~iLae~~~~~~~~~~ia~~il~ki~~~~~k~~~~~~~~~~~~l~~~~~~~~~vtd~~~~~~~af~fL   82 (219)
                      .|+|+|||||||++|||||+..+|||..+++++|+++|+.++|.+++.++|.|||+.++|++|+|+||.+||+++||.||
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            38999999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhcCCCCccccccccchHHHhHHHHHhchhhcCCchhhhHHHHHHHHHHhHHHHHHHhHHHHHhhhHHHHHH
Q 027768           83 ERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELL  162 (219)
Q Consensus        83 ~~i~~~f~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~~dkl~~i~~~l~~vk~im~~Ni~~vl~Rge~L~~l  162 (219)
                      ++|+++|.+.|+ ..+.++.|++++.+|++.|++.|++|+ +|.+.|++.+++++|+||++||.+||+++|+|||+||.|
T Consensus        81 ~~i~~eF~~~~~-~~~~~~~~~~~~~~f~~~l~~~~~~y~-d~~~~d~l~~~~~~l~ev~~im~~Ni~~vl~Rge~l~~L  158 (189)
T 4b93_A           81 NEVKKRFQTTYG-SRAQTALPYAMNSEFSSVLAAQLKHHS-ENKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELL  158 (189)
T ss_dssp             HHHHHHHHHHHG-GGGGTCCTTTTHHHHHHHHHHHHHHHH-CC-------CCHHHHHTTTTCCEECCCCBCTTSSBCCCC
T ss_pred             HHHHHHHHhhcc-ccccccCCccccchhhHHHHHHHHhhh-cccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHH
Confidence            999999999995 456677788888999999999999994 666679999999999999999999999999999999999


Q ss_pred             HHHhhhHHHHHHHHHHhHHHHHHHHHHHHhH
Q 027768          163 VDKTENLRSQAQDFRQQGTKMRRKMWIQNMK  193 (219)
Q Consensus       163 ~~ks~~L~~~s~~f~~~a~~l~~~~~~~~~k  193 (219)
                      ++||++|+.+|..|+++|++|+|+|||+|+|
T Consensus       159 ~~ks~~L~~~s~~f~~~a~~l~r~mwwkn~K  189 (189)
T 4b93_A          159 IDKTENLVDSSVTFKTTSRNLARAMCMKNIK  189 (189)
T ss_dssp             EETTCC-------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999999999999999999999987
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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_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
>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
>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
>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
>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
>2kog_A Vesicle-associated membrane protein 2; synaptobrevin, VAMP2, DPC micelle, snare, coiled coil, membrane fusion, transmembrane; NMR {Rattus norvegicus} 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
>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

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 219
d1ifqa_127 d.110.4.1 (A:) Sec22b {Mouse (Mus musculus) [TaxId 1e-22
d1ioua_140 d.110.4.1 (A:) Synaptobrevin homolog 1 ykt6 {Baker 6e-14
d2fh5a1129 d.110.4.4 (A:1-129) Signal recognition particle re 5e-04
>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 = 86.8 bits (215), Expect = 1e-22
 Identities = 27/125 (21%), Positives = 54/125 (43%), Gaps = 12/125 (9%)

Query: 5   SLIYSFVARGT--VILAEYTEFTGNFT-------SIASQCLQKLPA-TNNKFTYNCDGHT 54
           S++ + +AR    + LA   +             S A Q  +KL   +  + T      T
Sbjct: 1   SVLLTMIARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMT 60

Query: 55  FNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNK--EFGS 112
           F+Y++E G  Y V+   +  +++  A+LE +  +F++++G      +   S  +   F  
Sbjct: 61  FHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQ 120

Query: 113 KLKEH 117
           K K+ 
Sbjct: 121 KTKKL 125
>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 ?
Query219
d1ifqa_127 Sec22b {Mouse (Mus musculus) [TaxId: 10090]} 99.93
d1ioua_140 Synaptobrevin homolog 1 ykt6 {Baker's yeast (Sacch 99.76
d2fh5a1129 Signal recognition particle receptor alpha subunit 97.81
d2vgls_142 Sigma2 adaptin (clathrin coat assembly protein AP1 95.42
d2vglm2141 Mu2 adaptin (clathrin coat assembly protein AP50) 95.38
>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=99.93  E-value=1.2e-25  Score=163.62  Aligned_cols=116  Identities=22%  Similarity=0.402  Sum_probs=100.8

Q ss_pred             ceEEEEEEeCC--eEEEeecCCCCC-------HHHHHHHHhccCCCC-CCeeEEEECCeEEEEEeeCCEEEEEEecCCcc
Q 027768            5 SLIYSFVARGT--VILAEYTEFTGN-------FTSIASQCLQKLPAT-NNKFTYNCDGHTFNYLVENGFTYCVVAVESAG   74 (219)
Q Consensus         5 ~i~Ya~Iar~~--~iLae~~~~~~~-------~~~ia~~il~ki~~~-~~k~~~~~~~~~~~~l~~~~~~~~~vtd~~~~   74 (219)
                      +|+|++|||++  .+|+|+++.+++       +..+|+.++++++|+ ++|.+++.++|.|||++++|++|+|+||++||
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            48999999975  799999866543       345788999999876 58999999999999999999999999999999


Q ss_pred             cchHHHHHHHHHHHHhhhcCCCCccccccccchHHHhHHHHHhchhh
Q 027768           75 RQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYC  121 (219)
Q Consensus        75 ~~~af~fL~~i~~~f~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~  121 (219)
                      +++||.||++|+++|.+.|+........||+| .+|+..|++.++.|
T Consensus        81 ~~laF~fLeei~~eF~~~y~~~i~~~~rpy~F-i~Fd~~iqk~k~~y  126 (127)
T d1ifqa_          81 KKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSF-IEFDTFIQKTKKLY  126 (127)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTTTTTCCSTTTT-GGGHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhhhhhhhcccCCcch-HHHHHHHHHHHHhc
Confidence            99999999999999999996433334579999 68999999998776
>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