Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionQ9CQP2
DateWed Jul 10 14:24:44 BST 2013
Unique Job IDf74afb2e11cfc573
SequenceMSGSFYFVIV ... Download FASTA

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:36.374 Y:41.444 Z:34.937
Model (left) based on template d2j3wa1
Top template information
Fold:Profilin-like
Superfamily:SNARE-like
Family:Sedlin (SEDL)
Confidence and coverage
Confidence:100.0% Coverage:100%
140 residues (100% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MSGSFYFVIVGHHDNPVFEMEFLPPGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMY
Secondary structure 
SS confidence 
Disorder  ????
???????????
???????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  LKTVDKFNEWFVSAFVTAGHMRFIMLHDVRQEDGIKNFFTDVYDLYIKFAMNPFYEPNSP
Secondary structure 
SS confidence 
Disorder 
??
???
Disorder confidence 
 
   .........130.........140
Sequence  IRSSAFDRKVQFLGKKHLLS
Secondary structure 
SS confidence 
Disorder 
?
????
Disorder confidence 
 

Confidence Key
High(9)                    Low (0)
?Disordered ( 26%)
Alpha helix ( 39%)
Beta strand ( 28%)

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 2j3w chain A domain 1

3D model

Region: 1 - 140
Aligned: 140
Modelled: 140
Confidence: 100.0%
Identity: 100%
Fold: Profilin-like
Superfamily: SNARE-like
Family: Sedlin (SEDL)

Phyre2

PDB 2j3t chain C

3D model

Region: 3 - 136
Aligned: 133
Modelled: 134
Confidence: 100.0%
Identity: 11%
PDB header:transport
Chain: C: PDB Molecule:trafficking protein particle complex subunit 1;
PDBTitle: the crystal structure of the bet3-trs33-bet5-trs23 complex.

Phyre2

PDB 3cue chain M

3D model

Region: 3 - 136
Aligned: 133
Modelled: 134
Confidence: 100.0%
Identity: 18%
PDB header:protein transport
Chain: M: PDB Molecule:transport protein particle 23 kda subunit;
PDBTitle: crystal structure of a trapp subassembly activating the rab ypt1p

Phyre2

PDB 3pr6 chain A

3D model

Region: 6 - 130
Aligned: 115
Modelled: 125
Confidence: 100.0%
Identity: 17%
PDB header:transport protein
Chain: A: PDB Molecule:trapp-associated protein tca17;
PDBTitle: crystal structure analysis of yeast trapp associate protein tca17

Phyre2

PDB 2zmv chain B

3D model

Region: 3 - 136
Aligned: 132
Modelled: 122
Confidence: 100.0%
Identity: 26%
PDB header:transport protein
Chain: B: PDB Molecule:trafficking protein particle complex subunit 4;
PDBTitle: crystal structure of synbindin

Phyre2

PDB 3cue chain O

3D model

Region: 3 - 134
Aligned: 124
Modelled: 123
Confidence: 100.0%
Identity: 19%
PDB header:protein transport
Chain: O: PDB Molecule:transport protein particle 18 kda subunit;
PDBTitle: crystal structure of a trapp subassembly activating the rab ypt1p

Phyre2

PDB 3kyq chain A

3D model

Region: 1 - 137
Aligned: 129
Modelled: 137
Confidence: 94.3%
Identity: 8%
PDB header:transferase
Chain: A: PDB Molecule:synaptobrevin homolog ykt6;
PDBTitle: lipid-induced conformational switch controls fusion activity of longin2 domain snare ykt6

Phyre2

PDB 1gw5 chain M domain 2

3D model

Region: 6 - 112
Aligned: 91
Modelled: 92
Confidence: 91.2%
Identity: 13%
Fold: Profilin-like
Superfamily: SNARE-like
Family: Clathrin coat assembly domain

Phyre2

PDB 1iou chain A

3D model

Region: 1 - 137
Aligned: 131
Modelled: 137
Confidence: 86.6%
Identity: 7%
Fold: Profilin-like
Superfamily: SNARE-like
Family: Synatpobrevin N-terminal domain

Phyre2

PDB 2hf6 chain A

3D model

Region: 1 - 114
Aligned: 99
Modelled: 100
Confidence: 84.3%
Identity: 6%
PDB header:protein transport
Chain: A: PDB Molecule:coatomer subunit zeta-1;
PDBTitle: solution structure of human zeta-cop

Phyre2

PDB 2dmw chain A

3D model

Region: 1 - 137
Aligned: 116
Modelled: 121
Confidence: 63.7%
Identity: 13%
PDB header:membrane protein
Chain: A: PDB Molecule:synaptobrevin-like 1 variant;
PDBTitle: solution structure of the longin domain of synaptobrevin-2 like protein 1

Phyre2

PDB 2jkr chain M

3D model

Region: 6 - 110
Aligned: 89
Modelled: 90
Confidence: 63.4%
Identity: 13%
PDB header:endocytosis
Chain: M: PDB Molecule:ap-2 complex subunit mu-1;
PDBTitle: ap2 clathrin adaptor core with dileucine peptide rm(2 phosphos)qikrllse

Phyre2

PDB 3egd chain C

3D model

Region: 62 - 137
Aligned: 75
Modelled: 76
Confidence: 61.7%
Identity: 9%
PDB header:protein transport
Chain: C: PDB Molecule:vesicle-trafficking protein sec22b;
PDBTitle: crystal structure of the mammalian copii-coat protein2 sec23a/24a complexed with the snare protein sec22 and bound3 to the transport signal sequence of vesicular stomatitis4 virus glycoprotein

Phyre2

PDB 2nup chain C

3D model

Region: 62 - 137
Aligned: 75
Modelled: 76
Confidence: 61.7%
Identity: 9%
PDB header:protein transport
Chain: C: PDB Molecule:vesicle-trafficking protein sec22b;
PDBTitle: crystal structure of the human sec23a/24a heterodimer,2 complexed with the snare protein sec22b

Phyre2

PDB 1w63 chain P

3D model

Region: 6 - 110
Aligned: 90
Modelled: 90
Confidence: 47.0%
Identity: 3%
PDB header:endocytosis
Chain: P: PDB Molecule:adaptor-related protein complex 1, mu 1 subunit;
PDBTitle: ap1 clathrin adaptor core

Phyre2

PDB 4b93 chain A

3D model

Region: 1 - 137
Aligned: 116
Modelled: 123
Confidence: 42.7%
Identity: 13%
PDB header:exocytosis
Chain: A: PDB Molecule:vesicle-associated membrane protein 7;
PDBTitle: complex of vamp7 cytoplasmic domain with 2nd ankyrin repeat2 domain of varp

Phyre2

PDB 1ifq chain A

3D model

Region: 4 - 138
Aligned: 126
Modelled: 135
Confidence: 40.3%
Identity: 10%
Fold: Profilin-like
Superfamily: SNARE-like
Family: Synatpobrevin N-terminal domain

Phyre2

PDB 1mp9 chain B

3D model

Region: 56 - 113
Aligned: 56
Modelled: 58
Confidence: 21.0%
Identity: 11%
PDB header:dna binding protein
Chain: B: PDB Molecule:tata-binding protein;
PDBTitle: tbp from a mesothermophilic archaeon, sulfolobus2 acidocaldarius

Phyre2

PDB 1gw5 chain S

3D model

Region: 6 - 112
Aligned: 93
Modelled: 107
Confidence: 20.4%
Identity: 11%
Fold: Profilin-like
Superfamily: SNARE-like
Family: Clathrin coat assembly domain

Phyre2

PDB 4b0a chain A

3D model

Region: 57 - 109
Aligned: 51
Modelled: 53
Confidence: 18.0%
Identity: 14%
PDB header:transcription
Chain: A: PDB Molecule:transcription initiation factor tfiid subunit 1, linker,
PDBTitle: the high-resolution structure of ytbp-ytaf1 identifies2 conserved and competing interaction surfaces in3 transcriptional activation

Phyre2
1
d2j3wa1
2
c2j3tC_
3
c3cueM_
4
c3pr6A_
5
c2zmvB_
6
c3cueO_
7
c3kyqA_
8
d1gw5m2
9
d1ioua_
10
c2hf6A_
11
c2dmwA_
12
c2jkrM_
13
c3egdC_
14
c2nupC_
15
c1w63P_
16
c4b93A_
17
d1ifqa_
18
c1mp9B_
19
d1gw5s_
20
c4b0aA_
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d2j3wa1
100.0 100 Fold:Profilin-like
Superfamily:SNARE-like
Family:Sedlin (SEDL)
2c2j3tC_
100.0 11 PDB header:transport
Chain: C: PDB Molecule:trafficking protein particle complex subunit 1;
PDBTitle: the crystal structure of the bet3-trs33-bet5-trs23 complex.
3c3cueM_
100.0 18 PDB header:protein transport
Chain: M: PDB Molecule:transport protein particle 23 kda subunit;
PDBTitle: crystal structure of a trapp subassembly activating the rab ypt1p
4c3pr6A_
100.0 17 PDB header:transport protein
Chain: A: PDB Molecule:trapp-associated protein tca17;
PDBTitle: crystal structure analysis of yeast trapp associate protein tca17
5c2zmvB_
100.0 26 PDB header:transport protein
Chain: B: PDB Molecule:trafficking protein particle complex subunit 4;
PDBTitle: crystal structure of synbindin
6c3cueO_
100.0 19 PDB header:protein transport
Chain: O: PDB Molecule:transport protein particle 18 kda subunit;
PDBTitle: crystal structure of a trapp subassembly activating the rab ypt1p
7c3kyqA_
94.3 8 PDB header:transferase
Chain: A: PDB Molecule:synaptobrevin homolog ykt6;
PDBTitle: lipid-induced conformational switch controls fusion activity of longin2 domain snare ykt6
8d1gw5m2
91.2 13 Fold:Profilin-like
Superfamily:SNARE-like
Family:Clathrin coat assembly domain
9d1ioua_
86.6 7 Fold:Profilin-like
Superfamily:SNARE-like
Family:Synatpobrevin N-terminal domain
10c2hf6A_
84.3 6 PDB header:protein transport
Chain: A: PDB Molecule:coatomer subunit zeta-1;
PDBTitle: solution structure of human zeta-cop
11c2dmwA_
63.7 13 PDB header:membrane protein
Chain: A: PDB Molecule:synaptobrevin-like 1 variant;
PDBTitle: solution structure of the longin domain of synaptobrevin-2 like protein 1
12c2jkrM_
63.4 13 PDB header:endocytosis
Chain: M: PDB Molecule:ap-2 complex subunit mu-1;
PDBTitle: ap2 clathrin adaptor core with dileucine peptide rm(2 phosphos)qikrllse
13c3egdC_
61.7 9 PDB header:protein transport
Chain: C: PDB Molecule:vesicle-trafficking protein sec22b;
PDBTitle: crystal structure of the mammalian copii-coat protein2 sec23a/24a complexed with the snare protein sec22 and bound3 to the transport signal sequence of vesicular stomatitis4 virus glycoprotein
14c2nupC_
61.7 9 PDB header:protein transport
Chain: C: PDB Molecule:vesicle-trafficking protein sec22b;
PDBTitle: crystal structure of the human sec23a/24a heterodimer,2 complexed with the snare protein sec22b
15c1w63P_
47.0 3 PDB header:endocytosis
Chain: P: PDB Molecule:adaptor-related protein complex 1, mu 1 subunit;
PDBTitle: ap1 clathrin adaptor core
16c4b93A_
42.7 13 PDB header:exocytosis
Chain: A: PDB Molecule:vesicle-associated membrane protein 7;
PDBTitle: complex of vamp7 cytoplasmic domain with 2nd ankyrin repeat2 domain of varp
17d1ifqa_
40.3 10 Fold:Profilin-like
Superfamily:SNARE-like
Family:Synatpobrevin N-terminal domain
18c1mp9B_
21.0 11 PDB header:dna binding protein
Chain: B: PDB Molecule:tata-binding protein;
PDBTitle: tbp from a mesothermophilic archaeon, sulfolobus2 acidocaldarius
19d1gw5s_
20.4 11 Fold:Profilin-like
Superfamily:SNARE-like
Family:Clathrin coat assembly domain
20c4b0aA_
18.0 14 PDB header:transcription
Chain: A: PDB Molecule:transcription initiation factor tfiid subunit 1, linker,
PDBTitle: the high-resolution structure of ytbp-ytaf1 identifies2 conserved and competing interaction surfaces in3 transcriptional activation
21c1d3uA_
not modelled 17.7 8 PDB header:gene regulation/dna
Chain: A: PDB Molecule:tata-binding protein;
PDBTitle: tata-binding protein/transcription factor (ii)b/bre+tata-2 box complex from pyrococcus woesei
22c4eiyA_
not modelled 17.5 23 PDB header:membrane protein
Chain: A: PDB Molecule:adenosine receptor a2a/soluble cytochrome b562 chimera;
PDBTitle: crystal structure of the chimeric protein of a2aar-bril in complex2 with zm241385 at 1.8a resolution
23c1yd6A_
not modelled 17.4 13 PDB header:dna binding protein
Chain: A: PDB Molecule:uvrc;
PDBTitle: crystal structure of the giy-yig n-terminal endonuclease2 domain of uvrc from bacillus caldotenax
24c1rm1A_
not modelled 17.1 14 PDB header:transcription/dna
Chain: A: PDB Molecule:tata-box binding protein;
PDBTitle: structure of a yeast tfiia/tbp/tata-box dna complex
25c1ngmM_
not modelled 17.1 14 PDB header:transcription/dna
Chain: M: PDB Molecule:transcription initiation factor tfiid;
PDBTitle: crystal structure of a yeast brf1-tbp-dna ternary complex
26c1w63T_
not modelled 15.2 6 PDB header:endocytosis
Chain: T: PDB Molecule:adapter-related protein complex 1 sigma 1a
PDBTitle: ap1 clathrin adaptor core
27c2z8uQ_
not modelled 13.6 10 PDB header:transcription
Chain: Q: PDB Molecule:tata-box-binding protein;
PDBTitle: methanococcus jannaschii tbp
28d1e0na_
not modelled 13.6 17 Fold:WW domain-like
Superfamily:WW domain
Family:WW domain
29c3eikB_
not modelled 12.9 14 PDB header:transcription
Chain: B: PDB Molecule:tata-box-binding protein;
PDBTitle: double stranded dna binding protein
30c3trjC_
not modelled 11.5 10 PDB header:isomerase
Chain: C: PDB Molecule:phosphoheptose isomerase;
PDBTitle: structure of a phosphoheptose isomerase from francisella tularensis
31c3bcyA_
not modelled 10.9 39 PDB header:unknown function
Chain: A: PDB Molecule:protein yer067w;
PDBTitle: crystal structure of yer067w
32c3emlA_
not modelled 10.6 24 PDB header:membrane protein, receptor
Chain: A: PDB Molecule:human adenosine a2a receptor/t4 lysozyme chimera;
PDBTitle: the 2.6 a crystal structure of a human a2a adenosine receptor bound to2 zm241385.
33c4ax2A_
not modelled 9.5 27 PDB header:toxin
Chain: A: PDB Molecule:rap1b;
PDBTitle: new type vi-secreted toxins and self-resistance proteins in2 serratia marcescens
34d1qnaa2
not modelled 9.2 10 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
35d2cxha1
not modelled 9.0 22 Fold:Anticodon-binding domain-like
Superfamily:Class II aaRS ABD-related
Family:Brix domain
36c2cxhA_
not modelled 9.0 22 PDB header:rna binding protein
Chain: A: PDB Molecule:probable brix-domain ribosomal biogenesis protein;
PDBTitle: crystal structure of probable ribosomal biogenesis protein from2 aeropyrum pernix k1
37d1cdwa2
not modelled 7.4 10 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
38d1es6a1
not modelled 7.1 29 Fold:EV matrix protein
Superfamily:EV matrix protein
Family:EV matrix protein
39c3tcqA_
not modelled 6.9 29 PDB header:viral protein
Chain: A: PDB Molecule:matrix protein vp40;
PDBTitle: crystal structure of matrix protein vp40 from ebola virus sudan
40d1h2ca_
not modelled 6.9 29 Fold:EV matrix protein
Superfamily:EV matrix protein
Family:EV matrix protein
41c3rzeA_
not modelled 6.8 30 PDB header:hydrolase
Chain: A: PDB Molecule:histamine h1 receptor, lysozyme chimera;
PDBTitle: structure of the human histamine h1 receptor in complex with doxepin
42c1h2dA_
not modelled 6.7 29 PDB header:virus/viral protein
Chain: A: PDB Molecule:matrix protein vp40;
PDBTitle: ebola virus matrix protein vp40 n-terminal domain in2 complex with rna (low-resolution vp40[31-212] variant).
43c2go51_
not modelled 6.5 10 PDB header:translation/rna
Chain: 1: PDB Molecule:signal recognition particle receptor alpha
PDBTitle: structure of signal recognition particle receptor (sr) in2 complex with signal recognition particle (srp) and3 ribosome nascent chain complex
44d1d2zb_
not modelled 5.6 16 Fold:DEATH domain
Superfamily:DEATH domain
Family:DEATH domain, DD
45c1z5sD_
not modelled 5.1 23 PDB header:ligase
Chain: D: PDB Molecule:ran-binding protein 2;
PDBTitle: crystal structure of a complex between ubc9, sumo-1,2 rangap1 and nup358/ranbp2

Binding site prediction 

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If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite