Citrus Sinensis ID: 030595

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-----
MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQPFV
cccccEEEEEEEEccEEEEEEccccccHHHHHHHHHHcccccccEEEEEEccEEEEEEEEccEEEEEEEEcccccccHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccc
ccccHEEEEEEHcccEEEEEEccccccHHHHHHHHHHHccccccEEEEEcccEEEEEEEcccEEEEEEEccccccccHHHHHHHHHHHHHHHHccccHccHHHHHHcHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHccHHHHHHcccc
MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLqklpasnnkftyncdahtfnylvdngYTYCVVadessgrqipmAFLERVKDEfvskygggkaatapanglnkefgpKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKtenlhqqpfv
MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGgkaatapanglnKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIEllvdktenlhqqpfv
MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQPFV
*****LIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAAT****GLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLV************
**QKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCL*******NKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVD***************SEVKGVMMENIEKVLDRGEKIELLVD****L******
MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQPFV
**QKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQ***
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQPFV
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 ?
Query175 2.2.26 [Sep-21-2011]
Q9MAS5220 Putative vesicle-associat yes no 0.988 0.786 0.815 9e-82
P47192221 Vesicle-associated membra no no 0.988 0.782 0.815 2e-81
Q9ZTW3219 Vesicle-associated membra no no 0.988 0.789 0.803 8e-81
O48850285 Vesicle-associated membra no no 0.982 0.603 0.808 9e-81
O23429222 Vesicle-associated membra no no 0.988 0.779 0.678 5e-66
Q8VY69217 Vesicle-associated membra no no 0.925 0.746 0.697 1e-63
Q9M376240 Vesicle-associated membra no no 0.977 0.712 0.598 1e-62
Q9LFP1221 Vesicle-associated membra no no 0.96 0.760 0.418 1e-33
O49377219 Vesicle-associated membra no no 0.96 0.767 0.421 5e-33
Q86AQ7260 Vesicle-associated membra yes no 0.954 0.642 0.405 1e-31
>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 =  301 bits (772), Expect = 9e-82,   Method: Compositional matrix adjust.
 Identities = 141/173 (81%), Positives = 154/173 (89%)

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

Query: 61  NGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQY 120
           NG+TYCVV  ES+GRQIPMAFLERVK++F  +YGGGKA+TA AN LNKEFG KLKE MQY
Sbjct: 61  NGFTYCVVVIESAGRQIPMAFLERVKEDFNKRYGGGKASTAKANSLNKEFGSKLKEHMQY 120

Query: 121 CVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQP 173
           C DHPEEISKL+KVKAQV+EVKGVMMENIEKVLDRGEKIELLVDKTENL  Q 
Sbjct: 121 CADHPEEISKLSKVKAQVTEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQA 173
Involved in the targeting and/or fusion of transport vesicles to their target membrane.
Arabidopsis thaliana (taxid: 3702)
>sp|P47192|VA722_ARATH Vesicle-associated membrane protein 722 OS=Arabidopsis thaliana GN=VAMP722 PE=2 SV=2 Back     alignment and function description
>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|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|O49377|VA711_ARATH Vesicle-associated membrane protein 711 OS=Arabidopsis thaliana GN=VAMP711 PE=2 SV=2 Back     alignment and function description
>sp|Q86AQ7|VAM7B_DICDI Vesicle-associated membrane protein 7B OS=Dictyostelium discoideum GN=vamp7B PE=3 SV=1 Back     alignment and function description

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 ?
Query175
427199312219 vesicle-associated membrane protein 72 [ 0.982 0.785 0.918 1e-90
356532974221 PREDICTED: putative vesicle-associated m 0.982 0.778 0.924 2e-90
351727010221 uncharacterized protein LOC100500089 [Gl 0.982 0.778 0.912 1e-89
255638090221 unknown [Glycine max] 0.982 0.778 0.912 6e-89
224136560219 predicted protein [Populus trichocarpa] 0.982 0.785 0.901 8e-89
224115526221 predicted protein [Populus trichocarpa] 0.982 0.778 0.895 2e-88
356532978232 PREDICTED: putative vesicle-associated m 0.982 0.741 0.863 1e-87
388496790226 unknown [Lotus japonicus] 0.977 0.756 0.888 2e-87
255578566221 Vesicle-associated membrane protein, put 0.982 0.778 0.872 3e-87
449455429222 PREDICTED: putative vesicle-associated m 0.982 0.774 0.877 4e-87
>gi|427199312|gb|AFY26886.1| vesicle-associated membrane protein 72 [Morella rubra] Back     alignment and taxonomy information
 Score =  337 bits (863), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 158/172 (91%), Positives = 167/172 (97%)

Query: 1   MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVD 60
           MSQK LIYAFV+RG VVLAEYTEFSGNFNSIAYQCLQKLPA+NNKFTYNCD HTFNYLVD
Sbjct: 1   MSQKPLIYAFVSRGTVVLAEYTEFSGNFNSIAYQCLQKLPATNNKFTYNCDGHTFNYLVD 60

Query: 61  NGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQY 120
           NGYTYCVVADES GRQ+PMAFLER+KD+F+S+YGGGKA+TAPANGLNKEFGPKLKE M+Y
Sbjct: 61  NGYTYCVVADESVGRQVPMAFLERIKDDFLSRYGGGKASTAPANGLNKEFGPKLKEHMKY 120

Query: 121 CVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQ 172
           CVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQ
Sbjct: 121 CVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQ 172

Source: Morella rubra

Species: Morella rubra

Genus: Morella

Family: Myricaceae

Order: Fagales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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|224136560|ref|XP_002322360.1| predicted protein [Populus trichocarpa] gi|222869356|gb|EEF06487.1| predicted protein [Populus trichocarpa] 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|388496790|gb|AFK36461.1| unknown [Lotus japonicus] 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|449455429|ref|XP_004145455.1| PREDICTED: putative vesicle-associated membrane protein 726-like [Cucumis sativus] gi|449516904|ref|XP_004165486.1| PREDICTED: putative vesicle-associated membrane protein 726-like [Cucumis sativus] 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 ?
Query175
TAIR|locus:2010627220 VAMP726 "AT1G04760" [Arabidops 0.982 0.781 0.819 5.1e-74
TAIR|locus:2010642219 VAMP721 "AT1G04750" [Arabidops 0.982 0.785 0.808 4.6e-73
TAIR|locus:2046367285 VAMP725 "AT2G32670" [Arabidops 0.982 0.603 0.808 4.6e-73
TAIR|locus:2046595229 SAR1 "AT2G33120" [Arabidopsis 0.982 0.751 0.777 4.8e-71
TAIR|locus:2080340240 VAMP727 "AT3G54300" [Arabidops 0.531 0.387 0.655 2.6e-59
TAIR|locus:2046490217 VAMP723 "AT2G33110" [Arabidops 0.925 0.746 0.697 9.3e-59
TAIR|locus:2116672219 VAMP711 "vesicle-associated me 0.96 0.767 0.421 2e-31
TAIR|locus:2147952221 VAMP713 "AT5G11150" [Arabidops 0.96 0.760 0.418 4.2e-31
DICTYBASE|DDB_G0277173260 vamp7B "vesicle-associated mem 0.954 0.642 0.405 2.3e-30
TAIR|locus:2176342221 VAMP714 "AT5G22360" [Arabidops 0.96 0.760 0.377 4.4e-29
TAIR|locus:2010627 VAMP726 "AT1G04760" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 747 (268.0 bits), Expect = 5.1e-74, P = 5.1e-74
 Identities = 141/172 (81%), Positives = 154/172 (89%)

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

Query:    61 NGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQY 120
             NG+TYCVV  ES+GRQIPMAFLERVK++F  +YGGGKA+TA AN LNKEFG KLKE MQY
Sbjct:    61 NGFTYCVVVIESAGRQIPMAFLERVKEDFNKRYGGGKASTAKANSLNKEFGSKLKEHMQY 120

Query:   121 CVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLHQQ 172
             C DHPEEISKL+KVKAQV+EVKGVMMENIEKVLDRGEKIELLVDKTENL  Q
Sbjct:   121 CADHPEEISKLSKVKAQVTEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQ 172
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: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: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
DICTYBASE|DDB_G0277173 vamp7B "vesicle-associated membrane protein 7B" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
TAIR|locus:2176342 VAMP714 "AT5G22360" [Arabidopsis thaliana (taxid:3702)] 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) ?
Q9MAS5VA726_ARATHNo assigned EC number0.81500.98850.7863yesno

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 ?
Query175
pfam1377482 pfam13774, Longin, Regulated-SNARE-like domain 3e-29
pfam0095789 pfam00957, Synaptobrevin, Synaptobrevin 3e-20
COG5143190 COG5143, SNC1, Synaptobrevin/VAMP-like protein [In 5e-08
>gnl|CDD|222370 pfam13774, Longin, Regulated-SNARE-like domain Back     alignment and domain information 
 Score =  102 bits (257), Expect = 3e-29
 Identities = 34/82 (41%), Positives = 51/82 (62%), Gaps = 1/82 (1%)

Query: 31  IAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFV 90
           +A   L+KLP ++ + +Y    +TF+YLV++G  Y  +AD+   R++  AFLE +KDEF+
Sbjct: 1   VAKTILEKLPPNSPRQSYEEGNYTFHYLVEDGLCYLCIADKEYPRRLAFAFLEEIKDEFL 60

Query: 91  SKYGGGKAATAPANGLNKEFGP 112
            KYGG +AATA       EF  
Sbjct: 61  KKYGGSQAATASPYAFP-EFDT 81

Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain. Length = 82
>gnl|CDD|201526 pfam00957, Synaptobrevin, Synaptobrevin 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 175
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
COG5143190 SNC1 Synaptobrevin/VAMP-like protein [Intracellula 99.9
PF1377483 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3 99.87
KOG0860116 consensus Synaptobrevin/VAMP-like protein [Intrace 99.57
PF0095789 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 99.44
PF04086 279 SRP-alpha_N: Signal recognition particle, alpha su 95.37
PF09426141 Nyv1_N: Vacuolar R-SNARE Nyv1 N terminal; InterPro 95.11
KOG0781 587 consensus Signal recognition particle receptor, al 93.64
PF04099142 Sybindin: Sybindin-like family ; InterPro: IPR0072 93.64
COG5143190 SNC1 Synaptobrevin/VAMP-like protein [Intracellula 90.57
PF01217141 Clat_adaptor_s: Clathrin adaptor complex small cha 88.86
KOG0938 446 consensus Adaptor complexes medium subunit family 84.56
PF04628132 Sedlin_N: Sedlin, N-terminal conserved region; Int 80.29
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information 
Probab=100.00  E-value=2.9e-54  Score=312.85  Aligned_cols=169  Identities=73%  Similarity=1.123  Sum_probs=162.5

Q ss_pred             ccEEEEEEEcCCeeeeeeccCCCCHHHHHHHHHccCCCC-CCeeEEEeCCeEEEEEEeCCEEEEEEecCCCCcchHHHHH
Q 030595            4 KSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFL   82 (175)
Q Consensus         4 ~~I~Ya~Iar~~~iLae~~~~~~~~~~~~~~il~ki~~~-~~k~~~~~~~~~~h~~~~~~~~~~~it~~~~~~~~af~fL   82 (175)
                      |+|+|++||||++|||||++.+|||..++..+|+|+|++ ++|.+|.+|+|+|||+++||++|+|+++.+.++++||.||
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 6799999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhCCCCCCCCCCCCcccchhHHHHHHhhhhcCChhhhHHHHHHHHHHHHHHHHHHHhHHHHHHhhhhhHHH
Q 030595           83 ERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELL  162 (175)
Q Consensus        83 ~~i~~~F~~~~~~~~~~~~~~~~l~~~F~~~l~~~~~~y~~~~~~~d~l~~i~~~l~~v~~im~~ni~~il~Rge~l~~L  162 (175)
                      ++|++.|.+.|++. ++++.+|+++.+|++.|++.|++|.++|. .|++.+++.+++|||+||.+|||++|+|||+||.|
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 ERIKEDFKKRYGGG-AHTAVAYSMNKEFSSVLKQQMQYCSEHPE-ISKLAKVKAQVTEVKGVMMENIEKVLDRGEKIELL  158 (217)
T ss_pred             HHHHHHHHHHhccc-hhHHHHhHhHHHHHHHHHHHHHHHHcCcc-hhHHHHHHHHHHHHHHHHHHHHHHHHhccCeEEee
Confidence            99999999999744 78888999999999999999999988888 69999999999999999999999999999999999


Q ss_pred             HHhhHhhhcCCC
Q 030595          163 VDKTENLHQQPF  174 (175)
Q Consensus       163 ~~ks~~L~~~s~  174 (175)
                      ++||++|+.+|.
T Consensus       159 VdKTenl~~~s~  170 (217)
T KOG0859|consen  159 VDKTENLRSKSF  170 (217)
T ss_pred             echhhhhhhhhH
Confidence            999999998763

>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
>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
>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
>PF04086 SRP-alpha_N: Signal recognition particle, alpha subunit, N-terminal; InterPro: IPR007222 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ] Back     alignment and domain information
>PF09426 Nyv1_N: Vacuolar R-SNARE Nyv1 N terminal; InterPro: IPR019005 This entry represents the N-terminal domain of vacuolar R-SNARE Nyv1, which adopts a longin fold [] Back     alignment and domain information
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>PF04099 Sybindin: Sybindin-like family ; InterPro: IPR007233 Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses Back     alignment and domain information
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion] 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
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query175
4b93_A189 Complex Of Vamp7 Cytoplasmic Domain With 2nd Ankyri 7e-28
2dmw_A131 Solution Structure Of The Longin Domain Of Synaptob 9e-15
4afi_A173 Complex Between Vamp7 Longin Domain And Fragment Of 4e-14
2vx8_A169 Vamp7 Longin Domain Hrb Peptide Complex Length = 16 6e-14
2nup_C196 Crystal Structure Of The Human Sec23a24A HETERODIME 8e-09
3kyq_A199 Lipid-Induced Conformational Switch Controls Fusion 1e-06
3egd_C157 Crystal Structure Of The Mammalian Copii-Coat Prote 1e-05
2nps_A74 Crystal Structure Of The Early Endosomal Snare Comp 9e-05
3b5n_A61 Structure Of The Yeast Plasma Membrane Snare Comple 7e-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 =  119 bits (299), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 63/167 (37%), Positives = 98/167 (58%), Gaps = 6/167 (3%)
Query: 5   SLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYT 64
           ++++A VARG  +LA++    GNF  +  Q L K+P+ NNK TY+   + F+Y+  +   
Sbjct: 3   AILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIV 62
Query: 65  YCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDH 124
           Y  + D+   R    +FL  VK  F + Y G +A TA    +N EF   L   +++   H
Sbjct: 63  YLCITDDDFERSRAFSFLNEVKKRFQTTY-GSRAQTALPYAMNSEFSSVLAAQLKH---H 118
Query: 125 PE--EISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENL 169
            E   + K+ + +AQV E+KG+M+ NI+ V  RGE++ELL+DKTENL
Sbjct: 119 SENKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLIDKTENL 165
>pdb|2DMW|A Chain A, Solution Structure Of The Longin Domain Of Synaptobrevin- Like Protein 1 Length = 131 Back     alignment and structure
>pdb|4AFI|A Chain A, Complex Between Vamp7 Longin Domain And Fragment Of Delta- Adaptin From Ap3 Length = 173 Back     alignment and structure
>pdb|2VX8|A Chain A, Vamp7 Longin Domain Hrb Peptide Complex Length = 169 Back     alignment and structure
>pdb|2NUP|C Chain C, Crystal Structure Of The Human Sec23a24A HETERODIMER, Complexed With The Snare Protein Sec22b Length = 196 Back     alignment and structure
>pdb|3KYQ|A Chain A, Lipid-Induced Conformational Switch Controls Fusion Activity Of Longin Domain Snare Ykt6 Length = 199 Back     alignment and structure
>pdb|3EGD|C Chain C, Crystal Structure Of The Mammalian Copii-Coat Protein Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22 AND BOUND To The Transport Signal Sequence Of Vesicular Stomatitis Virus Glycoprotein Length = 157 Back     alignment and structure
>pdb|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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query175
4afi_A173 AP-3 complex subunit delta-1, vesicle-associated p 1e-46
2vx8_A169 Nucleoporin-like protein RIP, vesicle-associated m 2e-44
2nut_C196 Vesicle-trafficking protein SEC22B; human copii SE 6e-38
3kyq_A199 YKT6, synaptobrevin homolog YKT6; V-snare homolog, 2e-33
3b5n_A61 Synaptobrevin homolog 1; snare complex, syntaxin, 3e-18
1n7s_A63 Vesicle-associated membrane protein 2; neuronal sn 7e-18
1sfc_A96 VAMP 2, protein (synaptobrevin 2); membrane fusion 7e-17
2kog_A119 Vesicle-associated membrane protein 2; synaptobrev 8e-17
1l4a_A80 Synaptobrevin; snare, snare complex, membrane fusi 1e-16
1gl2_A65 Endobrevin; membrane protein, membrane fusion prot 6e-16
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 1e-14
2nps_A74 VAMP-4, vesicle-associated membrane protein 4; ves 2e-14
>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 =  149 bits (377), Expect = 1e-46
 Identities = 38/124 (30%), Positives = 64/124 (51%), Gaps = 1/124 (0%)

Query: 1   MSQKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVD 60
               ++++A VARG  +LA++    GNF  +  Q L K+P+ NNK TY+   + F+Y+  
Sbjct: 51  EEAMAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQ 110

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

Query: 121 CVDH 124
             ++
Sbjct: 170 HSEN 173
>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
>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
>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
>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
>1sfc_A VAMP 2, protein (synaptobrevin 2); membrane fusion protein complex, transport protein; 2.40A {Rattus norvegicus} SCOP: h.1.15.1 Length = 96 Back     alignment and structure
>2kog_A Vesicle-associated membrane protein 2; synaptobrevin, VAMP2, DPC micelle, snare, coiled coil, membrane fusion, transmembrane; NMR {Rattus norvegicus} Length = 119 Back     alignment and structure
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query175
4b93_A189 Vesicle-associated membrane protein 7; endocytosis 100.0
2nut_C196 Vesicle-trafficking protein SEC22B; human copii SE 100.0
3kyq_A199 YKT6, synaptobrevin homolog YKT6; V-snare homolog, 100.0
4afi_A173 AP-3 complex subunit delta-1, vesicle-associated p 100.0
2vx8_A169 Nucleoporin-like protein RIP, vesicle-associated m 99.98
3bw6_A144 Synaptobrevin homolog YKT6; YKT6P, farnesylation, 99.95
1gl2_A65 Endobrevin; membrane protein, membrane fusion prot 99.7
1l4a_A80 Synaptobrevin; snare, snare complex, membrane fusi 99.68
1n7s_A63 Vesicle-associated membrane protein 2; neuronal sn 99.67
3b5n_A61 Synaptobrevin homolog 1; snare complex, syntaxin, 99.66
2nps_A74 VAMP-4, vesicle-associated membrane protein 4; ves 99.65
1sfc_A96 VAMP 2, protein (synaptobrevin 2); membrane fusion 99.6
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 99.6
2kog_A119 Vesicle-associated membrane protein 2; synaptobrev 99.49
1urq_A63 M-tomosyn isoform; transport protein, tomosyn-snar 99.48
3zym_A310 Phosphatidylinositol-binding clathrin assembly PR 98.49
3fie_C38 Fragment of vesicle-associated membrane protein 2; 98.47
2fh5_A185 Signal recognition particle receptor alpha subunit 97.97
2fz0_A149 R-snare NYV1P, V-snare component of the vacuolar s 95.75
1w63_Q158 Adapter-related protein complex 1 sigma 1A subunit 93.33
2vgl_S142 AP-2 complex subunit sigma-1; cytoplasmic vesicle, 93.33
3tjz_C153 Coatomer subunit zeta-1; protein trafficking, golg 91.91
1w63_M 423 Adaptor-related protein complex 1, MU 1 subunit; e 91.2
2vgl_M 435 AP-2 complex subunit MU-1; cytoplasmic vesicle, al 90.31
2j3w_A142 Sedlin, trafficking protein particle complex prote 90.22
2j3t_C145 Trafficking protein particle complex subunit 1, tr 87.19
2j3t_D219 Trafficking protein particle complex subunit 4; tr 85.64
3cue_A219 Transport protein particle 23 kDa subunit; membran 84.04
3cue_C159 Transport protein particle 18 kDa subunit; membran 81.01
>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=5.3e-55  Score=325.93  Aligned_cols=170  Identities=36%  Similarity=0.610  Sum_probs=150.4

Q ss_pred             CccEEEEEEEcCCeeeeeeccCCCCHHHHHHHHHccCCCCCCeeEEEeCCeEEEEEEeCCEEEEEEecCCCCcchHHHHH
Q 030595            3 QKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFL   82 (175)
Q Consensus         3 ~~~I~Ya~Iar~~~iLae~~~~~~~~~~~~~~il~ki~~~~~k~~~~~~~~~~h~~~~~~~~~~~it~~~~~~~~af~fL   82 (175)
                      .|+|+|||||||++|||||+..+|||..+++.+|+++|+.++|++++.|+|.|||+.++|++|+|||+.+||+++||.||
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            48999999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhCCCCCCCCCCCCcccchhHHHHHHhhhhcCChhhhHHHHHHHHHHHHHHHHHHHhHHHHHHhhhhhHHH
Q 030595           83 ERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELL  162 (175)
Q Consensus        83 ~~i~~~F~~~~~~~~~~~~~~~~l~~~F~~~l~~~~~~y~~~~~~~d~l~~i~~~l~~v~~im~~ni~~il~Rge~l~~L  162 (175)
                      ++|+++|.+.|+ ..+.++.|++++.+|.+.|++.|++| ++|.+.|++.+++.+|+||++||.+||+++|+|||+||.|
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-SRAQTALPYAMNSEFSSVLAAQLKHH-SENKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELL  158 (189)
T ss_dssp             HHHHHHHHHHHG-GGGGTCCTTTTHHHHHHHHHHHHHHH-HCC-------CCHHHHHTTTTCCEECCCCBCTTSSBCCCC
T ss_pred             HHHHHHHHhhcc-ccccccCCccccchhhHHHHHHHHhh-hcccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHH
Confidence            999999999996 44667778888889999999999999 6777779999999999999999999999999999999999


Q ss_pred             HHhhHhhhcCCC
Q 030595          163 VDKTENLHQQPF  174 (175)
Q Consensus       163 ~~ks~~L~~~s~  174 (175)
                      ++||++|+.+|+
T Consensus       159 ~~ks~~L~~~s~  170 (189)
T 4b93_A          159 IDKTENLVDSSV  170 (189)
T ss_dssp             EETTCC------
T ss_pred             HHHHHHHHHHHH
Confidence            999999999886
>2nut_C Vesicle-trafficking protein SEC22B; human copii SEC23/24 complexed with SEC22, protein transport; 2.30A {Homo sapiens} PDB: 2nup_C 3egd_C 3egx_C 1ifq_A Back     alignment and structure
>3kyq_A YKT6, synaptobrevin homolog YKT6; V-snare homolog, lipid binding, cytoplasmic vesicle, ER-GOLG transport, golgi apparatus, lipoprotein; HET: DPV; 2.44A {Rattus norvegicus} Back     alignment and structure
>4afi_A AP-3 complex subunit delta-1, vesicle-associated protein 7; endocytosis, exocytosis, clathrin adaptor, chimera, fusion P; 2.80A {Homo sapiens} Back     alignment and structure
>2vx8_A Nucleoporin-like protein RIP, vesicle-associated membrane protein 7; endocytosis,exocytosis, endocytosis, exocytosis, acetylation, coiled coil; 2.2A {Homo sapiens} PDB: 2dmw_A Back     alignment and structure
>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
>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
>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
>1n7s_A Vesicle-associated membrane protein 2; neuronal snare protein complex, four helix bundle, transport protein; 1.45A {Rattus norvegicus} SCOP: h.1.15.1 PDB: 1kil_A 3rk2_A 3rk3_A 3rl0_A 3fii_B 3g94_B Back     alignment and structure
>3b5n_A Synaptobrevin homolog 1; snare complex, syntaxin, synaptobrevin, SNAP-25, SSO1P, SNC1P, SEC9P, SSO1, SNC1, coiled coil; 1.60A {Saccharomyces cerevisiae} SCOP: h.1.15.1 Back     alignment and structure
>2nps_A VAMP-4, vesicle-associated membrane protein 4; vesicle fusion, snare complex, early endosomal snare complex, VTI1A, VAMP4, transport protein; 2.50A {Mus musculus} Back     alignment and structure
>1sfc_A VAMP 2, protein (synaptobrevin 2); membrane fusion protein complex, transport protein; 2.40A {Rattus norvegicus} SCOP: h.1.15.1 Back     alignment and structure
>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
>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
>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
>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
>1w63_Q Adapter-related protein complex 1 sigma 1A subunit; endocytosis, clathrin adaptor, transport, coated PITS; 4.0A {Mus musculus} SCOP: i.23.1.1 Back     alignment and structure
>2vgl_S AP-2 complex subunit sigma-1; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Mus musculus} SCOP: i.23.1.1 PDB: 2jkt_I 2jkr_I* 2xa7_S Back     alignment and structure
>3tjz_C Coatomer subunit zeta-1; protein trafficking, golgi membrane, protein transport-prote binding complex; HET: GNP; 2.90A {Bos taurus} PDB: 2hf6_A Back     alignment and structure
>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
>2j3w_A Sedlin, trafficking protein particle complex protein 2; multisubunit tethering factor, trapp, palmitate, transport, lipoprotein; HET: PLM; 2.1A {Mus musculus} SCOP: d.110.4.3 PDB: 1h3q_A Back     alignment and structure
>2j3t_C Trafficking protein particle complex subunit 1, trafficking protein particle complex subunit 3; trapp, palmitate, transport, lipoprotein, ER-golgi transport apparatus, protein transport; HET: PLM; 2.4A {Mus musculus} Back     alignment and structure
>2j3t_D Trafficking protein particle complex subunit 4; trapp, palmitate, transport, lipoprotein, ER-golgi transport apparatus, protein transport; HET: PLM; 2.4A {Homo sapiens} PDB: 2zmv_A 2jsn_A Back     alignment and structure
>3cue_A Transport protein particle 23 kDa subunit; membrane traffic, GEF, tethering complex, RAB activation, GU nucleotide exchange factor; HET: PLM; 3.70A {Saccharomyces cerevisiae} Back     alignment and structure
>3cue_C Transport protein particle 18 kDa subunit; membrane traffic, GEF, tethering complex, RAB activation, GU nucleotide exchange factor; HET: PLM; 3.70A {Saccharomyces cerevisiae} Back     alignment and structure

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 175
d1ifqa_127 d.110.4.1 (A:) Sec22b {Mouse (Mus musculus) [TaxId 1e-24
d1ioua_140 d.110.4.1 (A:) Synaptobrevin homolog 1 ykt6 {Baker 7e-14
d2fh5a1129 d.110.4.4 (A:1-129) Signal recognition particle re 7e-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 = 91.0 bits (226), Expect = 1e-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 ?
Query175
d1ifqa_127 Sec22b {Mouse (Mus musculus) [TaxId: 10090]} 99.96
d1ioua_140 Synaptobrevin homolog 1 ykt6 {Baker's yeast (Sacch 99.86
d2fh5a1129 Signal recognition particle receptor alpha subunit 98.03
d2vglm2141 Mu2 adaptin (clathrin coat assembly protein AP50) 96.33
d2vgls_142 Sigma2 adaptin (clathrin coat assembly protein AP1 96.06
d2j3wa1140 Sedlin (SEDL) {Mouse (Mus musculus) [TaxId: 10090] 91.83
>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=99.96  E-value=5.3e-29  Score=172.08  Aligned_cols=115  Identities=24%  Similarity=0.413  Sum_probs=102.3

Q ss_pred             cEEEEEEEcCC--eeeeeeccCCCC-------HHHHHHHHHccCCCC-CCeeEEEeCCeEEEEEEeCCEEEEEEecCCCC
Q 030595            5 SLIYAFVARGN--VVLAEYTEFSGN-------FNSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDNGYTYCVVADESSG   74 (175)
Q Consensus         5 ~I~Ya~Iar~~--~iLae~~~~~~~-------~~~~~~~il~ki~~~-~~k~~~~~~~~~~h~~~~~~~~~~~it~~~~~   74 (175)
                      +|+|++|||++  +||||+++.+++       +.++++.++++++|+ +.|++++.++|.|||+.++|++|+|+||++||
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            58999999975  799999866543       345789999999876 68999999999999999999999999999999


Q ss_pred             cchHHHHHHHHHHHHHhhhCCCCCCC-CCCCCcccchhHHHHHHhhhh
Q 030595           75 RQIPMAFLERVKDEFVSKYGGGKAAT-APANGLNKEFGPKLKELMQYC  121 (175)
Q Consensus        75 ~~~af~fL~~i~~~F~~~~~~~~~~~-~~~~~l~~~F~~~l~~~~~~y  121 (175)
                      +++||.||++|+++|.+.|+. .+.+ .+||++ .+|+..|++.++.|
T Consensus        81 ~~laF~fLeei~~eF~~~y~~-~i~~~~rpy~F-i~Fd~~iqk~k~~y  126 (127)
T d1ifqa_          81 KKLAFAYLEDLHSEFDEQHGK-KVPTVSRPYSF-IEFDTFIQKTKKLY  126 (127)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTT-TTTTCCSTTTT-GGGHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhhhh-hhhcccCCcch-HHHHHHHHHHHHhc
Confidence            999999999999999999974 4544 579999 89999999999887
>d1ioua_ d.110.4.1 (A:) Synaptobrevin homolog 1 ykt6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2fh5a1 d.110.4.4 (A:1-129) Signal recognition particle receptor alpha subunit, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2j3wa1 d.110.4.3 (A:1-140) Sedlin (SEDL) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure