Phyre 2 Results for P62768

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Email | l.a.kelley@imperial.ac.uk
Description | P62768
Date | Thu Jan 5 12:07:50 GMT 2012
Unique Job ID | 8b0e5b8225681ef0

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2dnxA_
Top template information
PDB header:transport protein Chain: A: PDB Molecule:syntaxin-12; PDBTitle: solution structure of rsgi ruh-063, an n-terminal domain of2 syntaxin 12 from human cdna
Confidence and coverage
Confidence: | 32.4% | Coverage: | 52%
67 residues ( 52% of your sequence) have been modelled with 32.4% confidence by the single highest scoring template.
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3D viewing
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Sequence analysis |

Secondary structure and disorder prediction |

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Sequence |  | M | Y | D | N | L | K | S | L | G | I | T | N | P | E | E | I | D | R | Y | S | L | R | Q | E | A | N | N | D | I | L | K | I | Y | F | Q | K | D | K | G | E | F | F | A | K | S | V | K | F | K | Y | P | R | Q | R | K | T | V | V | A | D
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Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  | ? |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | G | V | G | Q | G | Y | K | E | V | Q | E | I | S | P | N | L | R | Y | I | I | D | E | L | D | Q | I | C | Q | R | D | R | S | E | V | D | L | K | R | K | I | L | D | D | L | R | H | L | E | S | V | V | T | N | K | I | S | E | I | E | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  | ? | ? |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | .
Sequence |  | D | L | E | K | L | T | R | K
Secondary structure |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |

Confidence Key
High(9) |  |  |  |  |  |  |  |  |  |  | Low (0)

? | Disordered
| Alpha helix
| Beta strand

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

Rank | Aligned region
--- | ---
1 |
| c2dnxA_ |

### PDB 2dnx chain A

Region: 58 - 125
Aligned: 67
Modelled: 68
Confidence: 32.4%
Identity: 16%
PDB header:transport protein
Chain: A: PDB Molecule:syntaxin-12;
PDBTitle: solution structure of rsgi ruh-063, an n-terminal domain of2 syntaxin 12 from human cdna

Phyre2
2 |
| c3t97B_ |

### PDB 3t97 chain B

Region: 87 - 126
Aligned: 40
Modelled: 40
Confidence: 27.8%
Identity: 15%
PDB header:protein transport
Chain: B: PDB Molecule:nuclear pore complex protein nup54;
PDBTitle: molecular architecture of the transport channel of the nuclear pore2 complex: nup62/nup54

Phyre2
3 |
| d1s94a_ |

### PDB 1s94 chain A

Region: 66 - 125
Aligned: 56
Modelled: 60
Confidence: 24.8%
Identity: 18%
Fold: STAT-like
Superfamily: t-snare proteins
Family: t-snare proteins

Phyre2
4 |
| c1s94A_ |

### PDB 1s94 chain A

Region: 66 - 125
Aligned: 56
Modelled: 60
Confidence: 24.8%
Identity: 18%
PDB header:endocytosis/exocytosis
Chain: A: PDB Molecule:s-syntaxin;
PDBTitle: crystal structure of the habc domain of neuronal syntaxin from the2 squid loligo pealei

Phyre2
5 |
| d2daha1 |

### PDB 2dah chain A domain 1

Region: 5 - 26
Aligned: 22
Modelled: 22
Confidence: 24.2%
Identity: 23%
Fold: RuvA C-terminal domain-like
Superfamily: UBA-like
Family: UBA domain

Phyre2
6 |
| d2dnaa1 |

### PDB 2dna chain A domain 1

Region: 5 - 26
Aligned: 22
Modelled: 22
Confidence: 23.6%
Identity: 14%
Fold: RuvA C-terminal domain-like
Superfamily: UBA-like
Family: UBA domain

Phyre2
7 |
| d2bwba1 |

### PDB 2bwb chain A domain 1

Region: 5 - 26
Aligned: 22
Modelled: 22
Confidence: 21.9%
Identity: 14%
Fold: RuvA C-terminal domain-like
Superfamily: UBA-like
Family: UBA domain

Phyre2
8 |
| c2cwbA_ |

### PDB 2cwb chain A

Region: 5 - 26
Aligned: 22
Modelled: 22
Confidence: 21.8%
Identity: 23%
PDB header:protein binding
Chain: A: PDB Molecule:chimera of immunoglobulin g binding protein g
PDBTitle: solution structure of the ubiquitin-associated domain of2 human bmsc-ubp and its complex with ubiquitin

Phyre2
9 |
| d1veja1 |

### PDB 1vej chain A domain 1

Region: 5 - 26
Aligned: 22
Modelled: 22
Confidence: 21.3%
Identity: 23%
Fold: RuvA C-terminal domain-like
Superfamily: UBA-like
Family: UBA domain

Phyre2
10 |
| c1wr1B_ |

### PDB 1wr1 chain B

Region: 5 - 26
Aligned: 22
Modelled: 22
Confidence: 20.4%
Identity: 14%
PDB header:signaling protein
Chain: B: PDB Molecule:ubiquitin-like protein dsk2;
PDBTitle: the complex sturcture of dsk2p uba with ubiquitin

Phyre2
11 |
| c1m1jA_ |

### PDB 1m1j chain A

Region: 58 - 123
Aligned: 66
Modelled: 66
Confidence: 18.5%
Identity: 14%
PDB header:blood clotting
Chain: A: PDB Molecule:fibrinogen alpha subunit;
PDBTitle: crystal structure of native chicken fibrinogen with two different2 bound ligands

Phyre2
12 |
| c1vp7D_ |

### PDB 1vp7 chain D

Region: 69 - 126
Aligned: 58
Modelled: 58
Confidence: 18.5%
Identity: 10%
PDB header:hydrolase
Chain: D: PDB Molecule:exodeoxyribonuclease vii small subunit;
PDBTitle: crystal structure of exodeoxyribonuclease vii small subunit2 (np_881400.1) from bordetella pertussis at 2.40 a resolution

Phyre2
13 |
| c2dnaA_ |

### PDB 2dna chain A

Region: 5 - 26
Aligned: 22
Modelled: 22
Confidence: 17.6%
Identity: 14%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:unnamed protein product;
PDBTitle: solution structure of rsgi ruh-056, a uba domain from mouse2 cdna

Phyre2
14 |
| c2dahA_ |

### PDB 2dah chain A

Region: 5 - 26
Aligned: 22
Modelled: 22
Confidence: 16.8%
Identity: 23%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:ubiquilin-3;
PDBTitle: solution structure of the c-terminal uba domain in the2 human ubiquilin 3

Phyre2
15 |
| c2jy5A_ |

### PDB 2jy5 chain A

Region: 5 - 26
Aligned: 22
Modelled: 22
Confidence: 16.0%
Identity: 18%
PDB header:signaling protein
Chain: A: PDB Molecule:ubiquilin-1;
PDBTitle: nmr structure of ubiquilin 1 uba domain

Phyre2
16 |
| c3a2aC_ |

### PDB 3a2a chain C

Region: 94 - 128
Aligned: 34
Modelled: 35
Confidence: 15.8%
Identity: 32%
PDB header:transport protein
Chain: C: PDB Molecule:voltage-gated hydrogen channel 1;
PDBTitle: the structure of the carboxyl-terminal domain of the human voltage-2 gated proton channel hv1

Phyre2
17 |
| c1deqO_ |

### PDB 1deq chain O

Region: 67 - 125
Aligned: 59
Modelled: 59
Confidence: 14.3%
Identity: 10%
PDB header:
PDB COMPND:

Phyre2
18 |
| c2eamA_ |

### PDB 2eam chain A

Region: 3 - 18
Aligned: 16
Modelled: 16
Confidence: 11.7%
Identity: 31%
PDB header:signaling protein
Chain: A: PDB Molecule:putative 47 kda protein;
PDBTitle: solution structure of the n-terminal sam-domain of a human2 putative 47 kda protein

Phyre2
19 |
| c1ydiB_ |

### PDB 1ydi chain B

Region: 105 - 122
Aligned: 18
Modelled: 18
Confidence: 11.6%
Identity: 22%
PDB header:cell adhesion, structural protein
Chain: B: PDB Molecule:alpha-actinin 4;
PDBTitle: human vinculin head domain (vh1, 1-258) in complex with2 human alpha-actinin's vinculin-binding site (residues 731-3 760)

Phyre2
20 |
| d1o5ha_ |

### PDB 1o5h chain A

Region: 54 - 124
Aligned: 66
Modelled: 71
Confidence: 10.4%
Identity: 15%
Fold: Methenyltetrahydrofolate cyclohydrolase-like
Superfamily: Methenyltetrahydrofolate cyclohydrolase-like
Family: Methenyltetrahydrofolate cyclohydrolase-like

Phyre2
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49 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2dnxA_ |
|  | 32.4 | 16 | PDB header:transport protein Chain: A: PDB Molecule:syntaxin-12; PDBTitle: solution structure of rsgi ruh-063, an n-terminal domain of2 syntaxin 12 from human cdna
2 | c3t97B_ |
|  | 27.8 | 15 | PDB header:protein transport Chain: B: PDB Molecule:nuclear pore complex protein nup54; PDBTitle: molecular architecture of the transport channel of the nuclear pore2 complex: nup62/nup54
3 | d1s94a_ |
|  | 24.8 | 18 | Fold:STAT-like Superfamily:t-snare proteins Family:t-snare proteins
4 | c1s94A_ |
|  | 24.8 | 18 | PDB header:endocytosis/exocytosis Chain: A: PDB Molecule:s-syntaxin; PDBTitle: crystal structure of the habc domain of neuronal syntaxin from the2 squid loligo pealei
5 | d2daha1 |
|  | 24.2 | 23 | Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain
6 | d2dnaa1 |
|  | 23.6 | 14 | Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain
7 | d2bwba1 |
|  | 21.9 | 14 | Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain
8 | c2cwbA_ |
|  | 21.8 | 23 | PDB header:protein binding Chain: A: PDB Molecule:chimera of immunoglobulin g binding protein g PDBTitle: solution structure of the ubiquitin-associated domain of2 human bmsc-ubp and its complex with ubiquitin
9 | d1veja1 |
|  | 21.3 | 23 | Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain
10 | c1wr1B_ |
|  | 20.4 | 14 | PDB header:signaling protein Chain: B: PDB Molecule:ubiquitin-like protein dsk2; PDBTitle: the complex sturcture of dsk2p uba with ubiquitin
11 | c1m1jA_ |
|  | 18.5 | 14 | PDB header:blood clotting Chain: A: PDB Molecule:fibrinogen alpha subunit; PDBTitle: crystal structure of native chicken fibrinogen with two different2 bound ligands
12 | c1vp7D_ |
|  | 18.5 | 10 | PDB header:hydrolase Chain: D: PDB Molecule:exodeoxyribonuclease vii small subunit; PDBTitle: crystal structure of exodeoxyribonuclease vii small subunit2 (np_881400.1) from bordetella pertussis at 2.40 a resolution
13 | c2dnaA_ |
|  | 17.6 | 14 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:unnamed protein product; PDBTitle: solution structure of rsgi ruh-056, a uba domain from mouse2 cdna
14 | c2dahA_ |
|  | 16.8 | 23 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ubiquilin-3; PDBTitle: solution structure of the c-terminal uba domain in the2 human ubiquilin 3
15 | c2jy5A_ |
|  | 16.0 | 18 | PDB header:signaling protein Chain: A: PDB Molecule:ubiquilin-1; PDBTitle: nmr structure of ubiquilin 1 uba domain
16 | c3a2aC_ |
|  | 15.8 | 32 | PDB header:transport protein Chain: C: PDB Molecule:voltage-gated hydrogen channel 1; PDBTitle: the structure of the carboxyl-terminal domain of the human voltage-2 gated proton channel hv1
17 | c1deqO_ |
|  | 14.3 | 10 | PDB header: PDB COMPND:
18 | c2eamA_ |
|  | 11.7 | 31 | PDB header:signaling protein Chain: A: PDB Molecule:putative 47 kda protein; PDBTitle: solution structure of the n-terminal sam-domain of a human2 putative 47 kda protein
19 | c1ydiB_ |
|  | 11.6 | 22 | PDB header:cell adhesion, structural protein Chain: B: PDB Molecule:alpha-actinin 4; PDBTitle: human vinculin head domain (vh1, 1-258) in complex with2 human alpha-actinin's vinculin-binding site (residues 731-3 760)
20 | d1o5ha_ |
|  | 10.4 | 15 | Fold:Methenyltetrahydrofolate cyclohydrolase-like Superfamily:Methenyltetrahydrofolate cyclohydrolase-like Family:Methenyltetrahydrofolate cyclohydrolase-like
21 | c1fllA_ |
| not modelled | 10.3 | 13 | PDB header:apoptosis Chain: A: PDB Molecule:tnf receptor associated factor 3; PDBTitle: molecular basis for cd40 signaling mediated by traf3
22 | c4a1cD_ |
| not modelled | 9.8 | 19 | PDB header:ribosome Chain: D: PDB Molecule:60s ribosomal protein l11; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 4.
23 | c2dl0A_ |
| not modelled | 9.5 | 31 | PDB header:signaling protein Chain: A: PDB Molecule:sam and sh3 domain-containing protein 1; PDBTitle: solution structure of the sam-domain of the sam and sh32 domain containing protein 1
24 | c1n73C_ |
| not modelled | 8.7 | 10 | PDB header:blood clotting Chain: C: PDB Molecule:fibrin gamma chain; PDBTitle: fibrin d-dimer, lamprey complexed with the peptide ligand: gly-his-2 arg-pro-amide
25 | c2k4pA_ |
| not modelled | 8.2 | 19 | PDB header:signaling protein Chain: A: PDB Molecule:phosphatidylinositol-3,4,5-trisphosphate 5- PDBTitle: solution structure of ship2-sam
26 | d1q08a_ |
| not modelled | 8.1 | 21 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators
27 | d1tafa_ |
| not modelled | 8.0 | 27 | Fold:Histone-fold Superfamily:Histone-fold Family:TBP-associated factors, TAFs
28 | d2pa2a1 |
| not modelled | 7.7 | 26 | Fold:alpha/beta-Hammerhead Superfamily:Ribosomal protein L16p/L10e Family:Ribosomal protein L10e
29 | c3c98B_ |
| not modelled | 7.5 | 12 | PDB header:endocytosis/exocytosis Chain: B: PDB Molecule:syntaxin-1a; PDBTitle: revised structure of the munc18a-syntaxin1 complex
30 | c2qkqA_ |
| not modelled | 7.4 | 19 | PDB header:transferase Chain: A: PDB Molecule:ephrin type-b receptor 4; PDBTitle: structure of the sam domain of human ephrin type-b receptor2 4
31 | d1xn7a_ |
| not modelled | 7.4 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Hypothetical protein YhgG
32 | c2d46A_ |
| not modelled | 7.3 | 58 | PDB header:metal transport Chain: A: PDB Molecule:calcium channel, voltage-dependent, beta 4 PDBTitle: solution structure of the human beta4a-a domain
33 | d1b0xa_ |
| not modelled | 7.2 | 31 | Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain
34 | c1b0xA_ |
| not modelled | 7.2 | 31 | PDB header:transferase Chain: A: PDB Molecule:protein (epha4 receptor tyrosine kinase); PDBTitle: the crystal structure of an eph receptor sam domain reveals2 a mechanism for modular dimerization.
35 | d1v38a_ |
| not modelled | 6.8 | 38 | Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain
36 | d1ug7a_ |
| not modelled | 6.8 | 46 | Fold:Four-helical up-and-down bundle Superfamily:Domain from hypothetical 2610208m17rik protein Family:Domain from hypothetical 2610208m17rik protein
37 | c2cp8A_ |
| not modelled | 6.7 | 15 | PDB header:protein binding Chain: A: PDB Molecule:next to brca1 gene 1 protein; PDBTitle: solution structure of the rsgi ruh-046, a uba domain from2 human next to brca1 gene 1 protein (kiaa0049 protein)3 r923h variant
38 | c2ke7A_ |
| not modelled | 6.6 | 31 | PDB header:protein binding Chain: A: PDB Molecule:ankyrin repeat and sterile alpha motif domain- PDBTitle: nmr structure of the first sam domain from aida1
39 | c1sfcD_ |
| not modelled | 6.1 | 18 | PDB header:transport protein Chain: D: PDB Molecule:protein (snap-25b); PDBTitle: neuronal synaptic fusion complex
40 | d1ez3a_ |
| not modelled | 6.0 | 17 | Fold:STAT-like Superfamily:t-snare proteins Family:t-snare proteins
41 | c2fxpA_ |
| not modelled | 5.8 | 15 | PDB header:viral protein Chain: A: PDB Molecule:spike glycoprotein; PDBTitle: solution structure of the sars-coronavirus hr2 domain
42 | c3dpqE_ |
| not modelled | 5.7 | 24 | PDB header:chaperone, peptide binding protein Chain: E: PDB Molecule:chaperone protein dnak; PDBTitle: crystal structure of the substrate binding domain of e.2 coli dnak in complex with a long pyrrhocoricin-derived3 inhibitor peptide (form b)
43 | c2e8nA_ |
| not modelled | 5.6 | 31 | PDB header:transferase, signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 2; PDBTitle: solution structure of the c-terminal sam-domain of ephaa2:2 ephrin type-a receptor 2 precursor (ec 2.7.10.1)
44 | c3pvpA_ |
| not modelled | 5.6 | 13 | PDB header:dna binding protein/dna Chain: A: PDB Molecule:chromosomal replication initiator protein dnaa; PDBTitle: structure of mycobacterium tuberculosis dnaa-dbd in complex with box22 dna
45 | c2npsD_ |
| not modelled | 5.5 | 19 | PDB header:transport protein Chain: D: PDB Molecule:syntaxin-6; PDBTitle: crystal structure of the early endosomal snare complex
46 | c2zshB_ |
| not modelled | 5.3 | 27 | PDB header:hormone receptor Chain: B: PDB Molecule:della protein gai; PDBTitle: structural basis of gibberellin(ga3)-induced della2 recognition by the gibberellin receptor
47 | d1sgga_ |
| not modelled | 5.3 | 13 | Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain
48 | d1gm5a1 |
| not modelled | 5.2 | 17 | Fold:Four-helical up-and-down bundle Superfamily:RecG, N-terminal domain Family:RecG, N-terminal domain
49 | c3zqsB_ |
| not modelled | 5.2 | 19 | PDB header:ligase Chain: B: PDB Molecule:e3 ubiquitin-protein ligase fancl; PDBTitle: human fancl central domain

Binding site prediction |

Due to computational demand, binding site predictions are not run for batch jobs

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

Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group
Imperial College London
Lawrence Kelley, Benjamin Jefferys
Disclaimer
Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0