Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP75687
DateThu Jan 5 12:13:08 GMT 2012
Unique Job ID7aab9e1326277242

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d2jnaa1
Top template information
Fold:Dodecin subunit-like
Superfamily:YdgH-like
Family:YdgH-like
Confidence and coverage
Confidence: 97.8% Coverage: 97%
76 residues ( 97% of your sequence) have been modelled with 97.8% 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  MFKKSVLFATLLSGVMAFSTNADDKIILKHISVSSVSASPTVLEDTIADIARKYNASSWK
Secondary structure 














SS confidence 



























































Disorder  ??????





?


??













??


?
?



















Disorder confidence 



























































 
   .........70........
Sequence  VTSMRIDNNSTATAVLYK
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

RankAligned region

PDB 2jna chain A domain 1

3D model

Region: 3 - 78
Aligned: 76
Modelled: 76
Confidence: 97.8%
Identity: 30%
Fold: Dodecin subunit-like
Superfamily: YdgH-like
Family: YdgH-like

Phyre2

PDB 2noc chain A domain 1

3D model

Region: 28 - 78
Aligned: 50
Modelled: 51
Confidence: 95.9%
Identity: 26%
Fold: Dodecin subunit-like
Superfamily: YdgH-like
Family: YdgH-like

Phyre2

PDB 2l69 chain A

3D model

Region: 39 - 56
Aligned: 18
Modelled: 18
Confidence: 25.3%
Identity: 50%
PDB header:de novo protein
Chain: A: PDB Molecule:rossmann 2x3 fold protein;
PDBTitle: solution nmr structure of de novo designed protein, p-loop ntpase2 fold, northeast structural genomics consortium target or28

Phyre2

PDB 1y7m chain A domain 2

3D model

Region: 45 - 57
Aligned: 13
Modelled: 13
Confidence: 20.4%
Identity: 38%
Fold: LysM domain
Superfamily: LysM domain
Family: LysM domain

Phyre2

PDB 1e0g chain A

3D model

Region: 45 - 57
Aligned: 13
Modelled: 13
Confidence: 18.8%
Identity: 23%
Fold: LysM domain
Superfamily: LysM domain
Family: LysM domain

Phyre2

PDB 2djp chain A

3D model

Region: 45 - 57
Aligned: 13
Modelled: 13
Confidence: 15.2%
Identity: 46%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein sb145;
PDBTitle: the solution structure of the lysm domain of human2 hypothetical protein sb145

Phyre2

PDB 3c7b chain B domain 2

3D model

Region: 45 - 63
Aligned: 19
Modelled: 19
Confidence: 14.9%
Identity: 37%
Fold: Ferredoxin-like
Superfamily: Nitrite/Sulfite reductase N-terminal domain-like
Family: DsrA/DsrB N-terminal-domain-like

Phyre2

PDB 1zj8 chain A domain 1

3D model

Region: 45 - 63
Aligned: 19
Modelled: 19
Confidence: 10.6%
Identity: 16%
Fold: Ferredoxin-like
Superfamily: Nitrite/Sulfite reductase N-terminal domain-like
Family: Duplicated SiR/NiR-like domains 1 and 3

Phyre2

PDB 4a1d chain K

3D model

Region: 43 - 55
Aligned: 13
Modelled: 13
Confidence: 9.5%
Identity: 62%
PDB header:ribosome
Chain: K: PDB Molecule:ubiquitin-60s ribosomal protein l40;
PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of3 molecule 4.

Phyre2

PDB 1xc0 chain A

3D model

Region: 5 - 15
Aligned: 11
Modelled: 11
Confidence: 8.6%
Identity: 73%
PDB header:signaling protein
Chain: A: PDB Molecule:pardaxin p-4;
PDBTitle: twenty lowest energy structures of pa4 by solution nmr

Phyre2

PDB 2v4j chain B domain 2

3D model

Region: 45 - 63
Aligned: 19
Modelled: 19
Confidence: 8.4%
Identity: 32%
Fold: Ferredoxin-like
Superfamily: Nitrite/Sulfite reductase N-terminal domain-like
Family: DsrA/DsrB N-terminal-domain-like

Phyre2

PDB 3sb1 chain B

3D model

Region: 21 - 53
Aligned: 33
Modelled: 33
Confidence: 8.0%
Identity: 18%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hydrogenase expression protein;
PDBTitle: hydrogenase expression protein huph from thiobacillus denitrificans2 atcc 25259

Phyre2
1

d2jnaa1
2

d2noca1
3

c2l69A_
4

d1y7ma2
5

d1e0ga_
6

c2djpA_
7

d3c7bb2
8

d1zj8a1
9

c4a1dK_
10

c1xc0A_
11

d2v4jb2
12

c3sb1B_



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d2jnaa1



97.8 30 Fold:Dodecin subunit-like
Superfamily:YdgH-like
Family:YdgH-like
2d2noca1



95.9 26 Fold:Dodecin subunit-like
Superfamily:YdgH-like
Family:YdgH-like
3c2l69A_



25.3 50 PDB header:de novo protein
Chain: A: PDB Molecule:rossmann 2x3 fold protein;
PDBTitle: solution nmr structure of de novo designed protein, p-loop ntpase2 fold, northeast structural genomics consortium target or28
4d1y7ma2



20.4 38 Fold:LysM domain
Superfamily:LysM domain
Family:LysM domain
5d1e0ga_



18.8 23 Fold:LysM domain
Superfamily:LysM domain
Family:LysM domain
6c2djpA_



15.2 46 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein sb145;
PDBTitle: the solution structure of the lysm domain of human2 hypothetical protein sb145
7d3c7bb2



14.9 37 Fold:Ferredoxin-like
Superfamily:Nitrite/Sulfite reductase N-terminal domain-like
Family:DsrA/DsrB N-terminal-domain-like
8d1zj8a1



10.6 16 Fold:Ferredoxin-like
Superfamily:Nitrite/Sulfite reductase N-terminal domain-like
Family:Duplicated SiR/NiR-like domains 1 and 3
9c4a1dK_



9.5 62 PDB header:ribosome
Chain: K: PDB Molecule:ubiquitin-60s ribosomal protein l40;
PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of3 molecule 4.
10c1xc0A_



8.6 73 PDB header:signaling protein
Chain: A: PDB Molecule:pardaxin p-4;
PDBTitle: twenty lowest energy structures of pa4 by solution nmr
11d2v4jb2



8.4 32 Fold:Ferredoxin-like
Superfamily:Nitrite/Sulfite reductase N-terminal domain-like
Family:DsrA/DsrB N-terminal-domain-like
12c3sb1B_



8.0 18 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hydrogenase expression protein;
PDBTitle: hydrogenase expression protein huph from thiobacillus denitrificans2 atcc 25259

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