Phyre 2 Results for P0AFX0

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Email | l.a.kelley@imperial.ac.uk
Description | P0AFX0
Date | Thu Jan 5 11:27:28 GMT 2012
Unique Job ID | a8714bc830adab46

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2rqlA_
Top template information
PDB header:translation Chain: A: PDB Molecule:probable sigma-54 modulation protein; PDBTitle: solution structure of the e. coli ribosome hibernation2 promoting factor hpf
Confidence and coverage
Confidence: | 100.0% | Coverage: | 100%
95 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 |  | M | Q | L | N | I | T | G | N | N | V | E | I | T | E | A | L | R | E | F | V | T | A | K | F | A | K | L | E | Q | Y | F | D | R | I | N | Q | V | Y | V | V | L | K | V | E | K | V | T | H | T | S | D | A | T | L | H | V | N | G | G | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | .
Sequence |  | I | H | A | S | A | E | G | Q | D | M | Y | A | A | I | D | G | L | I | D | K | L | A | R | Q | L | T | K | H | K | D | K | L | K | Q | H
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 |
| c2rqlA_ |

### PDB 2rql chain A

Region: 1 - 95
Aligned: 95
Modelled: 95
Confidence: 100.0%
Identity: 100%
PDB header:translation
Chain: A: PDB Molecule:probable sigma-54 modulation protein;
PDBTitle: solution structure of the e. coli ribosome hibernation2 promoting factor hpf

Phyre2
2 |
| d1imua_ |

### PDB 1imu chain A

Region: 1 - 95
Aligned: 95
Modelled: 95
Confidence: 100.0%
Identity: 34%
Fold: Ribosome binding protein Y (YfiA homologue)
Superfamily: Ribosome binding protein Y (YfiA homologue)
Family: Ribosome binding protein Y (YfiA homologue)

Phyre2
3 |
| c3tqmD_ |

### PDB 3tqm chain D

Region: 1 - 91
Aligned: 91
Modelled: 90
Confidence: 99.9%
Identity: 33%
PDB header:protein binding
Chain: D: PDB Molecule:ribosome-associated factor y;
PDBTitle: structure of an ribosomal subunit interface protein from coxiella2 burnetii

Phyre2
4 |
| d1l4sa_ |

### PDB 1l4s chain A

Region: 3 - 95
Aligned: 93
Modelled: 93
Confidence: 99.9%
Identity: 38%
Fold: Ribosome binding protein Y (YfiA homologue)
Superfamily: Ribosome binding protein Y (YfiA homologue)
Family: Ribosome binding protein Y (YfiA homologue)

Phyre2
5 |
| d2ywqa1 |

### PDB 2ywq chain A domain 1

Region: 3 - 89
Aligned: 86
Modelled: 87
Confidence: 99.9%
Identity: 33%
Fold: Ribosome binding protein Y (YfiA homologue)
Superfamily: Ribosome binding protein Y (YfiA homologue)
Family: Ribosome binding protein Y (YfiA homologue)

Phyre2
6 |
| d1sr9a3 |

### PDB 1sr9 chain A domain 3

Region: 33 - 81
Aligned: 49
Modelled: 49
Confidence: 24.2%
Identity: 22%
Fold: 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain
Superfamily: 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain
Family: 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain

Phyre2
7 |
| c3f6hA_ |

### PDB 3f6h chain A

Region: 49 - 81
Aligned: 33
Modelled: 33
Confidence: 23.6%
Identity: 21%
PDB header:transferase
Chain: A: PDB Molecule:alpha-isopropylmalate synthase;
PDBTitle: crystal structure of the regulatory domain of licms in2 complexed with isoleucine - type iii

Phyre2
8 |
| d1uila_ |

### PDB 1uil chain A

Region: 48 - 88
Aligned: 41
Modelled: 41
Confidence: 21.7%
Identity: 24%
Fold: dsRBD-like
Superfamily: dsRNA-binding domain-like
Family: Double-stranded RNA-binding domain (dsRBD)

Phyre2
9 |
| c3kxeD_ |

### PDB 3kxe chain D

Region: 9 - 25
Aligned: 17
Modelled: 17
Confidence: 19.9%
Identity: 18%
PDB header:protein binding
Chain: D: PDB Molecule:antitoxin protein pard-1;
PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex

Phyre2
10 |
| c1i7nA_ |

### PDB 1i7n chain A

Region: 7 - 85
Aligned: 75
Modelled: 77
Confidence: 19.7%
Identity: 13%
PDB header:neuropeptide
Chain: A: PDB Molecule:synapsin ii;
PDBTitle: crystal structure analysis of the c domain of synapsin ii2 from rat brain

Phyre2
11 |
| c2kxoA_ |

### PDB 2kxo chain A

Region: 2 - 59
Aligned: 58
Modelled: 58
Confidence: 19.2%
Identity: 10%
PDB header:cell cycle
Chain: A: PDB Molecule:cell division topological specificity factor;
PDBTitle: solution nmr structure of the cell division regulator mine protein2 from neisseria gonorrhoeae

Phyre2
12 |
| c1by0A_ |

### PDB 1by0 chain A

Region: 78 - 94
Aligned: 17
Modelled: 17
Confidence: 18.9%
Identity: 41%
PDB header:rna binding protein
Chain: A: PDB Molecule:protein (hepatitis delta antigen);
PDBTitle: n-terminal leucine-repeat region of hepatitis delta antigen

Phyre2
13 |
| c1pk8D_ |

### PDB 1pk8 chain D

Region: 10 - 81
Aligned: 68
Modelled: 72
Confidence: 18.0%
Identity: 9%
PDB header:membrane protein
Chain: D: PDB Molecule:rat synapsin i;
PDBTitle: crystal structure of rat synapsin i c domain complexed to2 ca.atp

Phyre2
14 |
| c2yh5A_ |

### PDB 2yh5 chain A

Region: 38 - 82
Aligned: 43
Modelled: 45
Confidence: 17.6%
Identity: 12%
PDB header:lipid binding protein
Chain: A: PDB Molecule:dapx protein;
PDBTitle: structure of the c-terminal domain of bamc

Phyre2
15 |
| d2clyc1 |

### PDB 2cly chain C domain 1

Region: 10 - 32
Aligned: 23
Modelled: 23
Confidence: 16.6%
Identity: 17%
Fold: Mitochondrial ATP synthase coupling factor 6
Superfamily: Mitochondrial ATP synthase coupling factor 6
Family: Mitochondrial ATP synthase coupling factor 6

Phyre2
16 |
| d2r85a2 |

### PDB 2r85 chain A domain 2

Region: 11 - 59
Aligned: 49
Modelled: 49
Confidence: 12.3%
Identity: 8%
Fold: ATP-grasp
Superfamily: Glutathione synthetase ATP-binding domain-like
Family: PurP ATP-binding domain-like

Phyre2
17 |
| d2hkja2 |

### PDB 2hkj chain A domain 2

Region: 65 - 94
Aligned: 30
Modelled: 30
Confidence: 12.2%
Identity: 23%
Fold: Ribosomal protein S5 domain 2-like
Superfamily: Ribosomal protein S5 domain 2-like
Family: DNA gyrase/MutL, second domain

Phyre2
18 |
| d1vzsa_ |

### PDB 1vzs chain A

Region: 7 - 31
Aligned: 25
Modelled: 25
Confidence: 11.0%
Identity: 20%
Fold: Mitochondrial ATP synthase coupling factor 6
Superfamily: Mitochondrial ATP synthase coupling factor 6
Family: Mitochondrial ATP synthase coupling factor 6

Phyre2
19 |
| c3r9jD_ |

### PDB 3r9j chain D

Region: 11 - 57
Aligned: 47
Modelled: 47
Confidence: 11.0%
Identity: 9%
PDB header:cell cycle,hydrolase/cell cycle
Chain: D: PDB Molecule:cell division topological specificity factor;
PDBTitle: 4.3a resolution structure of a mind-mine(i24n) protein complex

Phyre2
20 |
| c1mx0D_ |

### PDB 1mx0 chain D

Region: 65 - 94
Aligned: 30
Modelled: 30
Confidence: 10.8%
Identity: 23%
PDB header:isomerase
Chain: D: PDB Molecule:type ii dna topoisomerase vi subunit b;
PDBTitle: structure of topoisomerase subunit

Phyre2
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31 |
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34 |
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47 |
48 |
49 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2rqlA_ |
|  | 100.0 | 100 | PDB header:translation Chain: A: PDB Molecule:probable sigma-54 modulation protein; PDBTitle: solution structure of the e. coli ribosome hibernation2 promoting factor hpf
2 | d1imua_ |
|  | 100.0 | 34 | Fold:Ribosome binding protein Y (YfiA homologue) Superfamily:Ribosome binding protein Y (YfiA homologue) Family:Ribosome binding protein Y (YfiA homologue)
3 | c3tqmD_ |
|  | 99.9 | 33 | PDB header:protein binding Chain: D: PDB Molecule:ribosome-associated factor y; PDBTitle: structure of an ribosomal subunit interface protein from coxiella2 burnetii
4 | d1l4sa_ |
|  | 99.9 | 38 | Fold:Ribosome binding protein Y (YfiA homologue) Superfamily:Ribosome binding protein Y (YfiA homologue) Family:Ribosome binding protein Y (YfiA homologue)
5 | d2ywqa1 |
|  | 99.9 | 33 | Fold:Ribosome binding protein Y (YfiA homologue) Superfamily:Ribosome binding protein Y (YfiA homologue) Family:Ribosome binding protein Y (YfiA homologue)
6 | d1sr9a3 |
|  | 24.2 | 22 | Fold:2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain Superfamily:2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain Family:2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain
7 | c3f6hA_ |
|  | 23.6 | 21 | PDB header:transferase Chain: A: PDB Molecule:alpha-isopropylmalate synthase; PDBTitle: crystal structure of the regulatory domain of licms in2 complexed with isoleucine - type iii
8 | d1uila_ |
|  | 21.7 | 24 | Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD)
9 | c3kxeD_ |
|  | 19.9 | 18 | PDB header:protein binding Chain: D: PDB Molecule:antitoxin protein pard-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex
10 | c1i7nA_ |
|  | 19.7 | 13 | PDB header:neuropeptide Chain: A: PDB Molecule:synapsin ii; PDBTitle: crystal structure analysis of the c domain of synapsin ii2 from rat brain
11 | c2kxoA_ |
|  | 19.2 | 10 | PDB header:cell cycle Chain: A: PDB Molecule:cell division topological specificity factor; PDBTitle: solution nmr structure of the cell division regulator mine protein2 from neisseria gonorrhoeae
12 | c1by0A_ |
|  | 18.9 | 41 | PDB header:rna binding protein Chain: A: PDB Molecule:protein (hepatitis delta antigen); PDBTitle: n-terminal leucine-repeat region of hepatitis delta antigen
13 | c1pk8D_ |
|  | 18.0 | 9 | PDB header:membrane protein Chain: D: PDB Molecule:rat synapsin i; PDBTitle: crystal structure of rat synapsin i c domain complexed to2 ca.atp
14 | c2yh5A_ |
|  | 17.6 | 12 | PDB header:lipid binding protein Chain: A: PDB Molecule:dapx protein; PDBTitle: structure of the c-terminal domain of bamc
15 | d2clyc1 |
|  | 16.6 | 17 | Fold:Mitochondrial ATP synthase coupling factor 6 Superfamily:Mitochondrial ATP synthase coupling factor 6 Family:Mitochondrial ATP synthase coupling factor 6
16 | d2r85a2 |
|  | 12.3 | 8 | Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:PurP ATP-binding domain-like
17 | d2hkja2 |
|  | 12.2 | 23 | Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:DNA gyrase/MutL, second domain
18 | d1vzsa_ |
|  | 11.0 | 20 | Fold:Mitochondrial ATP synthase coupling factor 6 Superfamily:Mitochondrial ATP synthase coupling factor 6 Family:Mitochondrial ATP synthase coupling factor 6
19 | c3r9jD_ |
|  | 11.0 | 9 | PDB header:cell cycle,hydrolase/cell cycle Chain: D: PDB Molecule:cell division topological specificity factor; PDBTitle: 4.3a resolution structure of a mind-mine(i24n) protein complex
20 | c1mx0D_ |
|  | 10.8 | 23 | PDB header:isomerase Chain: D: PDB Molecule:type ii dna topoisomerase vi subunit b; PDBTitle: structure of topoisomerase subunit
21 | c2p0aA_ |
| not modelled | 10.2 | 17 | PDB header:neuropeptide Chain: A: PDB Molecule:synapsin-3; PDBTitle: the crystal structure of human synapsin iii (syn3) in complex with2 amppnp
22 | d2e9xd1 |
| not modelled | 9.8 | 20 | Fold:GINS helical bundle-like Superfamily:GINS helical bundle-like Family:SLD5 N-terminal domain-like
23 | c3r23B_ |
| not modelled | 9.7 | 18 | PDB header:ligase Chain: B: PDB Molecule:d-alanine--d-alanine ligase; PDBTitle: crystal structure of d-alanine--d-alanine ligase from bacillus2 anthracis
24 | d1hk8a_ |
| not modelled | 9.6 | 16 | Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:Class III anaerobic ribonucleotide reductase NRDD subunit
25 | c1hk8A_ |
| not modelled | 9.6 | 16 | PDB header:oxidoreductase Chain: A: PDB Molecule:anaerobic ribonucleotide-triphosphate reductase; PDBTitle: structural basis for allosteric substrate specificity2 regulation in class iii ribonucleotide reductases:3 nrdd in complex with dgtp
26 | c3l2iB_ |
| not modelled | 9.2 | 15 | PDB header:lyase Chain: B: PDB Molecule:3-dehydroquinate dehydratase; PDBTitle: 1.85 angstrom crystal structure of the 3-dehydroquinate dehydratase2 (arod) from salmonella typhimurium lt2.
27 | d1o6da_ |
| not modelled | 8.9 | 10 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like
28 | c3ehuA_ |
| not modelled | 8.3 | 19 | PDB header:membrane protein Chain: A: PDB Molecule:fusion protein of crfr1 extracellular domain and mbp; PDBTitle: crystal structure of the extracellular domain of human corticotropin2 releasing factor receptor type 1 (crfr1) in complex with crf
29 | d1sfla_ |
| not modelled | 8.2 | 24 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase
30 | d1gsoa3 |
| not modelled | 8.2 | 5 | Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:BC ATP-binding domain-like
31 | d2i52a1 |
| not modelled | 8.1 | 5 | Fold:MK0786-like Superfamily:MK0786-like Family:MK0786-like
32 | c3q2oB_ |
| not modelled | 7.6 | 15 | PDB header:lyase Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit; PDBTitle: crystal structure of purk: n5-carboxyaminoimidazole ribonucleotide2 synthetase
33 | c3rd6A_ |
| not modelled | 7.5 | 13 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:mll3558 protein; PDBTitle: crystal structure of mll3558 protein from rhizobium loti. northeast2 structural genomics consortium target id mlr403
34 | c1hf9B_ |
| not modelled | 7.4 | 31 | PDB header:atpase inhibitor Chain: B: PDB Molecule:atpase inhibitor (mitochondrial); PDBTitle: c-terminal coiled-coil domain from bovine if1
35 | d1lr0a_ |
| not modelled | 7.4 | 12 | Fold:TolA/TonB C-terminal domain Superfamily:TolA/TonB C-terminal domain Family:TolA
36 | c2yr1B_ |
| not modelled | 6.7 | 21 | PDB header:lyase Chain: B: PDB Molecule:3-dehydroquinate dehydratase; PDBTitle: crystal structure of 3-dehydroquinate dehydratase from geobacillus2 kaustophilus hta426
37 | d2r7ka2 |
| not modelled | 6.5 | 12 | Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:PurP ATP-binding domain-like
38 | d1xppa_ |
| not modelled | 6.1 | 13 | Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RBP11/RpoL
39 | c1q0vA_ |
| not modelled | 6.0 | 19 | PDB header:transport binding Chain: A: PDB Molecule:hydrophilic protein; has cysteine rich putative PDBTitle: solution structure of tandem uims of vps27
40 | d1ehia2 |
| not modelled | 6.0 | 12 | Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:ATP-binding domain of peptide synthetases
41 | c3e5nA_ |
| not modelled | 5.9 | 18 | PDB header:ligase Chain: A: PDB Molecule:d-alanine-d-alanine ligase a; PDBTitle: crystal strucutre of d-alanine-d-alanine ligase from2 xanthomonas oryzae pv. oryzae kacc10331
42 | c2l5gB_ |
| not modelled | 5.9 | 30 | PDB header:transcription regulator Chain: B: PDB Molecule:putative uncharacterized protein ncor2; PDBTitle: co-ordinates and 1h, 13c and 15n chemical shift assignments for the2 complex of gps2 53-90 and smrt 167-207
43 | c1a92B_ |
| not modelled | 5.9 | 35 | PDB header:leucine zipper Chain: B: PDB Molecule:delta antigen; PDBTitle: oligomerization domain of hepatitis delta antigen
44 | c2l9pA_ |
| not modelled | 5.7 | 11 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of q5hli9 from staphylococcus epidermidis,2 northeast structural genomics consortium target ser147
45 | c1g6uB_ |
| not modelled | 5.7 | 23 | PDB header:de novo protein Chain: B: PDB Molecule:domain swapped dimer; PDBTitle: crystal structure of a domain swapped dimer
46 | c1ulzA_ |
| not modelled | 5.7 | 10 | PDB header:ligase Chain: A: PDB Molecule:pyruvate carboxylase n-terminal domain; PDBTitle: crystal structure of the biotin carboxylase subunit of pyruvate2 carboxylase
47 | d1ghha_ |
| not modelled | 5.6 | 12 | Fold:DNA damage-inducible protein DinI Superfamily:DNA damage-inducible protein DinI Family:DNA damage-inducible protein DinI
48 | c3oqvA_ |
| not modelled | 5.4 | 11 | PDB header:protein binding Chain: A: PDB Molecule:albc; PDBTitle: albc, a cyclodipeptide synthase from streptomyces noursei
49 | c2q2eB_ |
| not modelled | 5.3 | 27 | PDB header:isomerase Chain: B: PDB Molecule:type 2 dna topoisomerase 6 subunit b; PDBTitle: crystal structure of the topoisomerase vi holoenzyme from2 methanosarcina mazei

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
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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