Citrus Sinensis ID: 029988

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----
MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQVNLAVADCLFRS
cccccEEEEEEEEccEEEEEEccccccHHHHHHHHHHccccccccEEEEEccEEEEEEEEccEEEEEEEEcccccccHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
ccccHEEHEEEHcccEEEEEEccccccHHHHHHHHHHHcccccccEEEEcccEEEEEEEcccEEEEEEEccHcccccHHHHHHHHHHHHHHHHcccHHcHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHccHHHHHHHHHHHHHHHHccc
MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLqklpatnnkftyncdghtfnylVENGFTYCVVAVESAGRQIPIAFLERVKEDFnkrygggkaATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQVNLAVADCLFRS
MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELlvdktenlrsqvnlavadclfrs
MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQVNLAVADCLFRS
*****LIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQVNLAVADCLF**
**QQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQ*LPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQ****************AQVSEVKGVMMENIEKVLDRGEKIELLV**************ADCLFR*
MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQVNLAVADCLFRS
**QQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQVNLAVADCLFR*
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQVNLAVADCLFRS
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 ?
Query184 2.2.26 [Sep-21-2011]
O48850285 Vesicle-associated membra yes no 0.934 0.603 0.912 3e-92
P47192221 Vesicle-associated membra no no 0.934 0.778 0.924 4e-92
Q9MAS5220 Putative vesicle-associat no no 0.934 0.781 0.912 4e-92
Q9ZTW3219 Vesicle-associated membra no no 0.934 0.785 0.912 1e-91
O23429222 Vesicle-associated membra no no 0.934 0.774 0.745 2e-73
Q8VY69217 Vesicle-associated membra no no 0.880 0.746 0.790 3e-72
Q9M376240 Vesicle-associated membra no no 0.945 0.725 0.606 2e-65
O49377219 Vesicle-associated membra no no 0.891 0.748 0.413 7e-33
Q9LFP1221 Vesicle-associated membra no no 0.891 0.742 0.410 9e-33
Q9SIQ9219 Vesicle-associated membra no no 0.891 0.748 0.383 2e-29
>sp|O48850|VA725_ARATH Vesicle-associated membrane protein 725 OS=Arabidopsis thaliana GN=VAMP725 PE=2 SV=2 Back     alignment and function desciption
 Score =  337 bits (863), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 157/172 (91%), Positives = 167/172 (97%)

Query: 1   MGQQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVE 60
           MGQQ+LIYSFVARGTVIL EYTEF GNFT++A+QCLQKLP++NNKFTYNCDGHTFNYLVE
Sbjct: 66  MGQQNLIYSFVARGTVILVEYTEFKGNFTAVAAQCLQKLPSSNNKFTYNCDGHTFNYLVE 125

Query: 61  NGFTYCVVAVESAGRQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQY 120
           NGFTYCVVAVES GRQIP+AFLERVKEDFNKRYGGGKA TA ANSLN+EFGSKLKEHMQY
Sbjct: 126 NGFTYCVVAVESVGRQIPMAFLERVKEDFNKRYGGGKATTAQANSLNREFGSKLKEHMQY 185

Query: 121 CVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQ 172
           CVDHP+EISKLAKVKAQV+EVKGVMMENIEKVLDRGEKIELLVDKTENLRSQ
Sbjct: 186 CVDHPDEISKLAKVKAQVTEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQ 237
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|Q9MAS5|VA726_ARATH Putative vesicle-associated membrane protein 726 OS=Arabidopsis thaliana GN=VAMP726 PE=3 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|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|O49377|VA711_ARATH Vesicle-associated membrane protein 711 OS=Arabidopsis thaliana GN=VAMP711 PE=2 SV=2 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|Q9SIQ9|VA712_ARATH Vesicle-associated membrane protein 712 OS=Arabidopsis thaliana GN=VAMP712 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 ?
Query184
449432442219 PREDICTED: putative vesicle-associated m 0.934 0.785 0.959 5e-94
255554170219 Vesicle-associated membrane protein, put 0.934 0.785 0.970 5e-94
224075615219 predicted protein [Populus trichocarpa] 0.934 0.785 0.965 1e-93
225462779220 PREDICTED: putative vesicle-associated m 0.934 0.781 0.965 2e-93
33347409194 synptobrevin-related protein [Pyrus pyri 0.934 0.886 0.953 2e-93
7211989229 Strong similarity to the synaptobrevin h 0.945 0.759 0.913 1e-91
449468628219 PREDICTED: putative vesicle-associated m 0.934 0.785 0.947 2e-91
225464234219 PREDICTED: putative vesicle-associated m 0.934 0.785 0.941 2e-91
192910812220 synaptobrevin 1 [Elaeis guineensis] 0.934 0.781 0.936 2e-91
297823047220 hypothetical protein ARALYDRAFT_482195 [ 0.934 0.781 0.924 5e-91
>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 =  348 bits (893), Expect = 5e-94,   Method: Compositional matrix adjust.
 Identities = 165/172 (95%), Positives = 172/172 (100%)

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 CVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQ 172
           C+DHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQ
Sbjct: 121 CLDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQ 172

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|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|33347409|gb|AAQ15287.1| synptobrevin-related protein [Pyrus pyrifolia] Back     alignment and taxonomy information
>gi|7211989|gb|AAF40460.1|AC004809_18 Strong similarity to the synaptobrevin homolog F25I18.14 gi|2924792 from A. thaliana on BAC gb|AC002334 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|449468628|ref|XP_004152023.1| PREDICTED: putative vesicle-associated membrane protein 726-like [Cucumis sativus] gi|449524754|ref|XP_004169386.1| PREDICTED: putative vesicle-associated membrane protein 726-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|225464234|ref|XP_002267063.1| PREDICTED: putative vesicle-associated membrane protein 726 isoform 1 [Vitis vinifera] gi|297744308|emb|CBI37278.3| 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|297823047|ref|XP_002879406.1| hypothetical protein ARALYDRAFT_482195 [Arabidopsis lyrata subsp. lyrata] gi|297325245|gb|EFH55665.1| hypothetical protein ARALYDRAFT_482195 [Arabidopsis lyrata subsp. lyrata] 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 ?
Query184
TAIR|locus:2010627220 VAMP726 "AT1G04760" [Arabidops 0.934 0.781 0.912 5e-83
TAIR|locus:2046367285 VAMP725 "AT2G32670" [Arabidops 0.934 0.603 0.912 8.2e-83
TAIR|locus:2010642219 VAMP721 "AT1G04750" [Arabidops 0.934 0.785 0.912 3.6e-82
TAIR|locus:2046595229 SAR1 "AT2G33120" [Arabidopsis 0.934 0.751 0.877 3.7e-80
TAIR|locus:2046490217 VAMP723 "AT2G33110" [Arabidops 0.880 0.746 0.790 7.4e-66
TAIR|locus:2080340240 VAMP727 "AT3G54300" [Arabidops 0.505 0.387 0.677 3.3e-61
TAIR|locus:2116672219 VAMP711 "vesicle-associated me 0.891 0.748 0.413 2e-31
TAIR|locus:2147952221 VAMP713 "AT5G11150" [Arabidops 0.891 0.742 0.410 2.3e-30
ZFIN|ZDB-GENE-040426-1055220 sybl1 "synaptobrevin-like 1" [ 0.885 0.740 0.375 2.4e-28
UNIPROTKB|F1NTP7178 VAMP7 "Vesicle-associated memb 0.896 0.926 0.385 3.9e-28
TAIR|locus:2010627 VAMP726 "AT1G04760" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 832 (297.9 bits), Expect = 5.0e-83, P = 5.0e-83
 Identities = 157/172 (91%), Positives = 167/172 (97%)

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 CVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENLRSQ 172
             C DHPEEISKL+KVKAQV+EVKGVMMENIEKVLDRGEKIELLVDKTENLRSQ
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:2046367 VAMP725 "AT2G32670" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2010642 VAMP721 "AT1G04750" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus: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
ZFIN|ZDB-GENE-040426-1055 sybl1 "synaptobrevin-like 1" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|F1NTP7 VAMP7 "Vesicle-associated membrane protein 7" [Gallus gallus (taxid:9031)] 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) ?
Q9ZTW3VA721_ARATHNo assigned EC number0.91270.93470.7853nono
O48850VA725_ARATHNo assigned EC number0.91270.93470.6035yesno
Q9MAS5VA726_ARATHNo assigned EC number0.91270.93470.7818nono
P47192VA722_ARATHNo assigned EC number0.92440.93470.7782nono

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
estExt_fgenesh4_pm.C_LG_III0602
hypothetical protein (219 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query184
pfam1377482 pfam13774, Longin, Regulated-SNARE-like domain 3e-27
pfam0095789 pfam00957, Synaptobrevin, Synaptobrevin 1e-19
COG5143190 COG5143, SNC1, Synaptobrevin/VAMP-like protein [In 7e-09
>gnl|CDD|222370 pfam13774, Longin, Regulated-SNARE-like domain Back     alignment and domain information 
 Score = 98.0 bits (245), Expect = 3e-27
 Identities = 32/82 (39%), Positives = 51/82 (62%), Gaps = 1/82 (1%)

Query: 31  IASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFLERVKEDFN 90
           +A   L+KLP  + + +Y    +TF+YLVE+G  Y  +A +   R++  AFLE +K++F 
Sbjct: 1   VAKTILEKLPPNSPRQSYEEGNYTFHYLVEDGLCYLCIADKEYPRRLAFAFLEEIKDEFL 60

Query: 91  KRYGGGKAATAVANSLNKEFGS 112
           K+YGG +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 184
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 99.93
PF1377483 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3 99.83
KOG0860116 consensus Synaptobrevin/VAMP-like protein [Intrace 99.68
PF0095789 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 99.61
PF09426141 Nyv1_N: Vacuolar R-SNARE Nyv1 N terminal; InterPro 95.25
PF04086 279 SRP-alpha_N: Signal recognition particle, alpha su 94.78
COG5143190 SNC1 Synaptobrevin/VAMP-like protein [Intracellula 94.49
PF04099142 Sybindin: Sybindin-like family ; InterPro: IPR0072 92.95
KOG0781 587 consensus Signal recognition particle receptor, al 92.6
PF04799171 Fzo_mitofusin: fzo-like conserved region; InterPro 86.33
KOG0938 446 consensus Adaptor complexes medium subunit family 85.31
PF01217141 Clat_adaptor_s: Clathrin adaptor complex small cha 82.14
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information 
Probab=100.00  E-value=1.5e-57  Score=334.20  Aligned_cols=175  Identities=77%  Similarity=1.117  Sum_probs=169.1

Q ss_pred             cceEEEEEEeCCeeEEeecCCCCCHHHHHHHHhccCCCC-CCeeEEEEcCeEEEEEeeCCEEEEEEeeCCCCcccHHHHH
Q 029988            4 QSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPAT-NNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFL   82 (184)
Q Consensus         4 m~i~ya~Iar~~~iLae~~~~~~~~~~~a~~vL~ki~~~-~~k~~~~~~~~~fh~l~~~~~~~v~vt~~~~~~~~af~fL   82 (184)
                      |+|+|++||||++|||||++++|||.+++.++|+|||.+ ++|++|.+|+|.|||+.+||++|+|+++++.++++||.||
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            799999999999999999999999999999999999976 6799999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCCCcccccccccchHHHHHHHHhhhhhcCChhHhHHHHHHHHHHHHHHHHHHHhHHHHHHhhhhhHHH
Q 029988           83 ERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELL  162 (184)
Q Consensus        83 ~~i~~~f~~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~~dkl~~~~~~l~~v~~im~~ni~~il~Rge~L~~L  162 (184)
                      ++|++.|.+.|+.. +.++.+++++.+|++.|++.|++|.++|. .|++.+++.+++|||+||.+|||++|+|||+||.|
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            99999999999975 78889999999999999999999988897 89999999999999999999999999999999999


Q ss_pred             HHhHHHHHHHHHHHhhhc
Q 029988          163 VDKTENLRSQVNLAVADC  180 (184)
Q Consensus       163 ~~kt~~L~~~s~~f~~~~  180 (184)
                      ++||++|+.+|..|++.+
T Consensus       159 VdKTenl~~~s~~fr~q~  176 (217)
T KOG0859|consen  159 VDKTENLRSKSFDFRTQG  176 (217)
T ss_pred             echhhhhhhhhHHHHHHH
Confidence            999999999999998865

>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
>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
>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
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion] 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
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [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
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query184
4b93_A189 Complex Of Vamp7 Cytoplasmic Domain With 2nd Ankyri 3e-29
4afi_A173 Complex Between Vamp7 Longin Domain And Fragment Of 2e-15
2vx8_A169 Vamp7 Longin Domain Hrb Peptide Complex Length = 16 4e-15
2dmw_A131 Solution Structure Of The Longin Domain Of Synaptob 2e-14
2nup_C196 Crystal Structure Of The Human Sec23a24A HETERODIME 7e-09
3kyq_A199 Lipid-Induced Conformational Switch Controls Fusion 6e-06
3egd_C157 Crystal Structure Of The Mammalian Copii-Coat Prote 3e-05
2nps_A74 Crystal Structure Of The Early Endosomal Snare Comp 9e-05
>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 =  124 bits (312), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 69/187 (36%), Positives = 109/187 (58%), Gaps = 14/187 (7%)
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--EISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELLVDKTENL--------RSQVN 174
            E   + K+ + +AQV E+KG+M+ NI+ V  RGE++ELL+DKTENL         +  N
Sbjct: 119 SENKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLIDKTENLVDSSVTFKTTSRN 178
Query: 175 LAVADCL 181
           LA A C+
Sbjct: 179 LARAMCM 185
>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|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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query184
4afi_A173 AP-3 complex subunit delta-1, vesicle-associated p 2e-47
2vx8_A169 Nucleoporin-like protein RIP, vesicle-associated m 7e-44
2nut_C196 Vesicle-trafficking protein SEC22B; human copii SE 3e-37
3kyq_A199 YKT6, synaptobrevin homolog YKT6; V-snare homolog, 2e-34
3b5n_A61 Synaptobrevin homolog 1; snare complex, syntaxin, 7e-18
1n7s_A63 Vesicle-associated membrane protein 2; neuronal sn 1e-17
1l4a_A80 Synaptobrevin; snare, snare complex, membrane fusi 6e-17
1sfc_A96 VAMP 2, protein (synaptobrevin 2); membrane fusion 4e-16
1gl2_A65 Endobrevin; membrane protein, membrane fusion prot 8e-16
2kog_A119 Vesicle-associated membrane protein 2; synaptobrev 2e-15
2nps_A74 VAMP-4, vesicle-associated membrane protein 4; ves 2e-14
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 3e-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 =  151 bits (383), Expect = 2e-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
>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
>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
>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
>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
>2kog_A Vesicle-associated membrane protein 2; synaptobrevin, VAMP2, DPC micelle, snare, coiled coil, membrane fusion, transmembrane; NMR {Rattus norvegicus} Length = 119 Back     alignment and structure
>2nps_A VAMP-4, vesicle-associated membrane protein 4; vesicle fusion, snare complex, early endosomal snare complex, VTI1A, VAMP4, transport protein; 2.50A {Mus musculus} Length = 74 Back     alignment and structure
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query184
4b93_A189 Vesicle-associated membrane protein 7; endocytosis 100.0
2nut_C196 Vesicle-trafficking protein SEC22B; human copii SE 100.0
3kyq_A199 YKT6, synaptobrevin homolog YKT6; V-snare homolog, 100.0
4afi_A173 AP-3 complex subunit delta-1, vesicle-associated p 100.0
2vx8_A169 Nucleoporin-like protein RIP, vesicle-associated m 99.97
3bw6_A144 Synaptobrevin homolog YKT6; YKT6P, farnesylation, 99.94
1gl2_A65 Endobrevin; membrane protein, membrane fusion prot 99.81
3b5n_A61 Synaptobrevin homolog 1; snare complex, syntaxin, 99.78
1n7s_A63 Vesicle-associated membrane protein 2; neuronal sn 99.78
2nps_A74 VAMP-4, vesicle-associated membrane protein 4; ves 99.77
3hd7_A91 Vesicle-associated membrane protein 2; membrane pr 99.74
1l4a_A80 Synaptobrevin; snare, snare complex, membrane fusi 99.73
1sfc_A96 VAMP 2, protein (synaptobrevin 2); membrane fusion 99.73
1urq_A63 M-tomosyn isoform; transport protein, tomosyn-snar 99.65
2kog_A119 Vesicle-associated membrane protein 2; synaptobrev 99.58
3zym_A310 Phosphatidylinositol-binding clathrin assembly PR 98.51
3fie_C38 Fragment of vesicle-associated membrane protein 2; 98.44
2fh5_A185 Signal recognition particle receptor alpha subunit 97.97
2fz0_A149 R-snare NYV1P, V-snare component of the vacuolar s 95.95
3tjz_C153 Coatomer subunit zeta-1; protein trafficking, golg 87.93
2vgl_S142 AP-2 complex subunit sigma-1; cytoplasmic vesicle, 86.05
1t3j_A96 Mitofusin 1; coiled coil antiparallel, dimer, memb 85.35
1w63_M 423 Adaptor-related protein complex 1, MU 1 subunit; e 83.51
2vgl_M 435 AP-2 complex subunit MU-1; cytoplasmic vesicle, al 83.15
1w63_Q158 Adapter-related protein complex 1 sigma 1A subunit 82.41
>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=5.8e-56  Score=335.66  Aligned_cols=176  Identities=35%  Similarity=0.585  Sum_probs=150.0

Q ss_pred             CcceEEEEEEeCCeeEEeecCCCCCHHHHHHHHhccCCCCCCeeEEEEcCeEEEEEeeCCEEEEEEeeCCCCcccHHHHH
Q 029988            3 QQSLIYSFVARGTVILAEYTEFTGNFTSIASQCLQKLPATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAGRQIPIAFL   82 (184)
Q Consensus         3 ~m~i~ya~Iar~~~iLae~~~~~~~~~~~a~~vL~ki~~~~~k~~~~~~~~~fh~l~~~~~~~v~vt~~~~~~~~af~fL   82 (184)
                      .|+|+|+|||||++|||||+..+|||.++++.+|+++|+.++++++++|+|.|||++++|++|+|||+.+||+++||.||
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            49999999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCCCcccccccccchHHHHHHHHhhhhhcCChhHhHHHHHHHHHHHHHHHHHHHhHHHHHHhhhhhHHH
Q 029988           83 ERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVLDRGEKIELL  162 (184)
Q Consensus        83 ~~i~~~f~~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~~dkl~~~~~~l~~v~~im~~ni~~il~Rge~L~~L  162 (184)
                      ++|+++|...|+.. +.++.+++.+.+|.+.|+++|++| +||...|++.+++++|+||++||.+||+++|+|||+||.|
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 NEVKKRFQTTYGSR-AQTALPYAMNSEFSSVLAAQLKHH-SENKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELL  158 (189)
T ss_dssp             HHHHHHHHHHHGGG-GGTCCTTTTHHHHHHHHHHHHHHH-HCC-------CCHHHHHTTTTCCEECCCCBCTTSSBCCCC
T ss_pred             HHHHHHHHhhcccc-ccccCCccccchhhHHHHHHHHhh-hcccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHH
Confidence            99999999999864 556678888899999999999999 5666789999999999999999999999999999999999


Q ss_pred             HHhHHHHHHHHHHHhhhc
Q 029988          163 VDKTENLRSQVNLAVADC  180 (184)
Q Consensus       163 ~~kt~~L~~~s~~f~~~~  180 (184)
                      ++||++|+.+|+.|++.+
T Consensus       159 ~~ks~~L~~~s~~f~~~a  176 (189)
T 4b93_A          159 IDKTENLVDSSVTFKTTS  176 (189)
T ss_dssp             EETTCC------------
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999999999999876
>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
>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
>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
>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
>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
>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
>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
>2kog_A Vesicle-associated membrane protein 2; synaptobrevin, VAMP2, DPC micelle, snare, coiled coil, membrane fusion, transmembrane; NMR {Rattus norvegicus} 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
>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
>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
>1t3j_A Mitofusin 1; coiled coil antiparallel, dimer, membrane protein; 2.50A {Mus musculus} SCOP: h.4.16.1 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
>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

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 184
d1ifqa_127 d.110.4.1 (A:) Sec22b {Mouse (Mus musculus) [TaxId 4e-23
d1ioua_140 d.110.4.1 (A:) Synaptobrevin homolog 1 ykt6 {Baker 5e-14
d2fh5a1129 d.110.4.4 (A:1-129) Signal recognition particle re 3e-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 = 87.1 bits (216), Expect = 4e-23
 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 ?
Query184
d1ifqa_127 Sec22b {Mouse (Mus musculus) [TaxId: 10090]} 99.96
d1ioua_140 Synaptobrevin homolog 1 ykt6 {Baker's yeast (Sacch 99.81
d2fh5a1129 Signal recognition particle receptor alpha subunit 97.92
d2vglm2141 Mu2 adaptin (clathrin coat assembly protein AP50) 95.72
d2vgls_142 Sigma2 adaptin (clathrin coat assembly protein AP1 94.94
d2j3wa1140 Sedlin (SEDL) {Mouse (Mus musculus) [TaxId: 10090] 87.62
>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=4e-28  Score=169.85  Aligned_cols=116  Identities=22%  Similarity=0.378  Sum_probs=102.3

Q ss_pred             ceEEEEEEeC--CeeEEeecCCCCC-------HHHHHHHHhccCC-CCCCeeEEEEcCeEEEEEeeCCEEEEEEeeCCCC
Q 029988            5 SLIYSFVARG--TVILAEYTEFTGN-------FTSIASQCLQKLP-ATNNKFTYNCDGHTFNYLVENGFTYCVVAVESAG   74 (184)
Q Consensus         5 ~i~ya~Iar~--~~iLae~~~~~~~-------~~~~a~~vL~ki~-~~~~k~~~~~~~~~fh~l~~~~~~~v~vt~~~~~   74 (184)
                      +|+|++|||+  ++|||++++.+++       +..+|+.+|++++ .++.++++..++|.|||++++|++|+|+|++++|
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            5899999997  4999999876554       3467899999996 4578999999999999999999999999999999


Q ss_pred             cccHHHHHHHHHHHHHhhcCCCCcccccccccchHHHHHHHHhhhhh
Q 029988           75 RQIPIAFLERVKEDFNKRYGGGKAATAVANSLNKEFGSKLKEHMQYC  121 (184)
Q Consensus        75 ~~~af~fL~~i~~~f~~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~y  121 (184)
                      +++||.||++|+++|...|+.. +.++.+|+.+.+|+.+|++.++.|
T Consensus        81 ~~laF~fLeei~~eF~~~y~~~-i~~~~rpy~Fi~Fd~~iqk~k~~y  126 (127)
T d1ifqa_          81 KKLAFAYLEDLHSEFDEQHGKK-VPTVSRPYSFIEFDTFIQKTKKLY  126 (127)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTT-TTTCCSTTTTGGGHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhhhhh-hhcccCCcchHHHHHHHHHHHHhc
Confidence            9999999999999999999864 556666666789999999999887
>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