Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionO52982
DateThu Jan 5 10:56:32 GMT 2012
Unique Job ID984a8762e1344498

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1ig8a1
Top template information
Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:Hexokinase
Confidence and coverage
Confidence: 40.6% Coverage: 45%
66 residues ( 45% of your sequence) have been modelled with 40.6% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
Please note: You must be registered and logged in to use Phyrealarm.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MKRKTLPLLALVATSLFLSACDDRSDDLKAISKFKDLTPPRFSDVVSRQDDVSEEWSQVG
Secondary structure 















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Disorder  ???????






































??


??




??
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   .........70.........80.........90.........100.........110.........120
Sequence  FSSGLTLQVLRTRESPDGCEGGSYYYLVDMEEKTVQPLMNALCIADNIKLEYHEVTDPYT
Secondary structure 























SS confidence 



























































Disorder 









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??????























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   .........130.........140.......
Sequence  KEKYFEYSHDGKLMGRLLIPSNPDNRE
Secondary structure 












SS confidence 


























Disorder 



















???????
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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

RankAligned region

PDB 1ig8 chain A domain 1

3D model

Region: 22 - 87
Aligned: 66
Modelled: 66
Confidence: 40.6%
Identity: 14%
Fold: Ribonuclease H-like motif
Superfamily: Actin-like ATPase domain
Family: Hexokinase

Phyre2

PDB 3fma chain D

3D model

Region: 54 - 80
Aligned: 26
Modelled: 27
Confidence: 30.5%
Identity: 27%
PDB header:protein binding
Chain: D: PDB Molecule:protein smy2;
PDBTitle: crystal structure of the gyf domain of smy2 in complex with a proline-2 rich peptide from bbp/scsf1

Phyre2

PDB 3d12 chain E

3D model

Region: 75 - 114
Aligned: 40
Modelled: 40
Confidence: 24.5%
Identity: 18%
PDB header:hydrolase/membrane protein
Chain: E: PDB Molecule:ephrin-b3;
PDBTitle: crystal structures of nipah virus g attachment glycoprotein in complex2 with its receptor ephrin-b3

Phyre2

PDB 1iko chain P

3D model

Region: 75 - 117
Aligned: 43
Modelled: 43
Confidence: 23.4%
Identity: 16%
Fold: Cupredoxin-like
Superfamily: Cupredoxins
Family: Ephrin ectodomain

Phyre2

PDB 1iko chain P

3D model

Region: 75 - 117
Aligned: 43
Modelled: 43
Confidence: 23.4%
Identity: 16%
PDB header:signaling protein
Chain: P: PDB Molecule:ephrin-b2;
PDBTitle: crystal structure of the murine ephrin-b2 ectodomain

Phyre2

PDB 3f1z chain F

3D model

Region: 82 - 94
Aligned: 13
Modelled: 13
Confidence: 23.1%
Identity: 62%
PDB header:dna binding protein
Chain: F: PDB Molecule:putative nucleic acid-binding lipoprotein;
PDBTitle: crystal structure of putative nucleic acid-binding lipoprotein2 (yp_001337197.1) from klebsiella pneumoniae subsp. pneumoniae mgh3 78578 at 2.46 a resolution

Phyre2

PDB 2jna chain A domain 1

3D model

Region: 80 - 92
Aligned: 13
Modelled: 13
Confidence: 15.2%
Identity: 38%
Fold: Dodecin subunit-like
Superfamily: YdgH-like
Family: YdgH-like

Phyre2

PDB 2v0x chain B

3D model

Region: 52 - 60
Aligned: 9
Modelled: 9
Confidence: 14.7%
Identity: 56%
PDB header:cell cycle
Chain: B: PDB Molecule:lamina-associated polypeptide 2 isoforms
PDBTitle: the dimerization domain of lap2alpha

Phyre2

PDB 1tu2 chain B domain 2

3D model

Region: 80 - 93
Aligned: 14
Modelled: 14
Confidence: 13.0%
Identity: 50%
Fold: Barrel-sandwich hybrid
Superfamily: Rudiment single hybrid motif
Family: Cytochrome f, small domain

Phyre2

PDB 1bg3 chain A domain 3

3D model

Region: 73 - 87
Aligned: 15
Modelled: 15
Confidence: 11.8%
Identity: 47%
Fold: Ribonuclease H-like motif
Superfamily: Actin-like ATPase domain
Family: Hexokinase

Phyre2

PDB 1j6w chain A

3D model

Region: 75 - 101
Aligned: 27
Modelled: 27
Confidence: 11.8%
Identity: 37%
Fold: LuxS/MPP-like metallohydrolase
Superfamily: LuxS/MPP-like metallohydrolase
Family: Autoinducer-2 production protein LuxS

Phyre2

PDB 1qfx chain A

3D model

Region: 18 - 82
Aligned: 65
Modelled: 65
Confidence: 11.7%
Identity: 15%
Fold: Phosphoglycerate mutase-like
Superfamily: Phosphoglycerate mutase-like
Family: Histidine acid phosphatase

Phyre2

PDB 1x9y chain A domain 2

3D model

Region: 77 - 88
Aligned: 12
Modelled: 12
Confidence: 11.4%
Identity: 58%
Fold: Cystatin-like
Superfamily: Cystatin/monellin
Family: Staphopain B, prodomain

Phyre2

PDB 2ph7 chain B

3D model

Region: 82 - 99
Aligned: 18
Modelled: 18
Confidence: 10.7%
Identity: 33%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein af_2093;
PDBTitle: crystal structure of af2093 from archaeoglobus fulgidus

Phyre2

PDB 1v4s chain A domain 1

3D model

Region: 73 - 87
Aligned: 15
Modelled: 15
Confidence: 10.4%
Identity: 40%
Fold: Ribonuclease H-like motif
Superfamily: Actin-like ATPase domain
Family: Hexokinase

Phyre2

PDB 1cza chain N domain 1

3D model

Region: 25 - 87
Aligned: 63
Modelled: 63
Confidence: 10.2%
Identity: 25%
Fold: Ribonuclease H-like motif
Superfamily: Actin-like ATPase domain
Family: Hexokinase

Phyre2

PDB 1m7k chain A

3D model

Region: 38 - 64
Aligned: 27
Modelled: 27
Confidence: 9.5%
Identity: 22%
Fold: Spectrin repeat-like
Superfamily: BAG domain
Family: BAG domain

Phyre2

PDB 1wh2 chain A

3D model

Region: 54 - 77
Aligned: 23
Modelled: 24
Confidence: 9.2%
Identity: 26%
Fold: GYF/BRK domain-like
Superfamily: GYF domain
Family: GYF domain

Phyre2

PDB 3zr8 chain X

3D model

Region: 47 - 74
Aligned: 28
Modelled: 28
Confidence: 8.8%
Identity: 25%
PDB header:protein binding
Chain: X: PDB Molecule:avr3a11;
PDBTitle: crystal structure of rxlr effector avr3a11 from phytophthora capsici

Phyre2

PDB 1cza chain N domain 3

3D model

Region: 28 - 87
Aligned: 60
Modelled: 60
Confidence: 8.4%
Identity: 22%
Fold: Ribonuclease H-like motif
Superfamily: Actin-like ATPase domain
Family: Hexokinase

Phyre2
1

d1ig8a1
2

c3fmaD_
3

c3d12E_
4

d1ikop_
5

c1ikoP_
6

c3f1zF_
7

d2jnaa1
8

c2v0xB_
9

d1tu2b2
10

d1bg3a3
11

d1j6wa_
12

d1qfxa_
13

d1x9ya2
14

c2ph7B_
15

d1v4sa1
16

d1czan1
17

d1m7ka_
18

d1wh2a_
19

c3zr8X_
20

d1czan3
21



22



23



24



25



26



27



28



29



30



31






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1ig8a1



40.6 14 Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:Hexokinase
2c3fmaD_



30.5 27 PDB header:protein binding
Chain: D: PDB Molecule:protein smy2;
PDBTitle: crystal structure of the gyf domain of smy2 in complex with a proline-2 rich peptide from bbp/scsf1
3c3d12E_



24.5 18 PDB header:hydrolase/membrane protein
Chain: E: PDB Molecule:ephrin-b3;
PDBTitle: crystal structures of nipah virus g attachment glycoprotein in complex2 with its receptor ephrin-b3
4d1ikop_



23.4 16 Fold:Cupredoxin-like
Superfamily:Cupredoxins
Family:Ephrin ectodomain
5c1ikoP_



23.4 16 PDB header:signaling protein
Chain: P: PDB Molecule:ephrin-b2;
PDBTitle: crystal structure of the murine ephrin-b2 ectodomain
6c3f1zF_



23.1 62 PDB header:dna binding protein
Chain: F: PDB Molecule:putative nucleic acid-binding lipoprotein;
PDBTitle: crystal structure of putative nucleic acid-binding lipoprotein2 (yp_001337197.1) from klebsiella pneumoniae subsp. pneumoniae mgh3 78578 at 2.46 a resolution
7d2jnaa1



15.2 38 Fold:Dodecin subunit-like
Superfamily:YdgH-like
Family:YdgH-like
8c2v0xB_



14.7 56 PDB header:cell cycle
Chain: B: PDB Molecule:lamina-associated polypeptide 2 isoforms
PDBTitle: the dimerization domain of lap2alpha
9d1tu2b2



13.0 50 Fold:Barrel-sandwich hybrid
Superfamily:Rudiment single hybrid motif
Family:Cytochrome f, small domain
10d1bg3a3



11.8 47 Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:Hexokinase
11d1j6wa_



11.8 37 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:Autoinducer-2 production protein LuxS
12d1qfxa_



11.7 15 Fold:Phosphoglycerate mutase-like
Superfamily:Phosphoglycerate mutase-like
Family:Histidine acid phosphatase
13d1x9ya2



11.4 58 Fold:Cystatin-like
Superfamily:Cystatin/monellin
Family:Staphopain B, prodomain
14c2ph7B_



10.7 33 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein af_2093;
PDBTitle: crystal structure of af2093 from archaeoglobus fulgidus
15d1v4sa1



10.4 40 Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:Hexokinase
16d1czan1



10.2 25 Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:Hexokinase
17d1m7ka_



9.5 22 Fold:Spectrin repeat-like
Superfamily:BAG domain
Family:BAG domain
18d1wh2a_



9.2 26 Fold:GYF/BRK domain-like
Superfamily:GYF domain
Family:GYF domain
19c3zr8X_



8.8 25 PDB header:protein binding
Chain: X: PDB Molecule:avr3a11;
PDBTitle: crystal structure of rxlr effector avr3a11 from phytophthora capsici
20d1czan3



8.4 22 Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:Hexokinase
21d1j6xa_



not modelled 8.2 22 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:Autoinducer-2 production protein LuxS
22c2hacA_



not modelled 7.6 36 PDB header:membrane protein
Chain: A: PDB Molecule:t-cell surface glycoprotein cd3 zeta chain;
PDBTitle: structure of zeta-zeta transmembrane dimer
23d2nn6g2



not modelled 7.2 35 Fold:Barrel-sandwich hybrid
Superfamily:Ribosomal L27 protein-like
Family:ECR1 N-terminal domain-like
24d1xn7a_



not modelled 7.0 53 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Hypothetical protein YhgG
25d1wd3a1



not modelled 6.6 33 Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Alpha-L-arabinofuranosidase B, N-terminal domain
26d3b2ua2



not modelled 6.3 71 Fold:Knottins (small inhibitors, toxins, lectins)
Superfamily:Growth factor receptor domain
Family:Growth factor receptor domain
27d1bdga1



not modelled 6.1 33 Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:Hexokinase
28d1uhza_



not modelled 5.9 17 Fold:dsRBD-like
Superfamily:dsRNA-binding domain-like
Family:Double-stranded RNA-binding domain (dsRBD)
29d2hsga1



not modelled 5.9 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
30c3njqB_



not modelled 5.6 12 PDB header:viral protein/inhibitor
Chain: B: PDB Molecule:orf 17;
PDBTitle: crystal structure of kaposi's sarcoma-associated herpesvirus protease2 in complex with dimer disruptor
31d1slqa_



not modelled 5.6 37 Fold:VP4 membrane interaction domain
Superfamily:VP4 membrane interaction domain
Family:VP4 membrane interaction 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