Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP77529
DateThu Jan 5 12:30:19 GMT 2012
Unique Job IDbcc5489b2ca5c18a

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d2nwwa1
Top template information
Fold:Proton glutamate symport protein
Superfamily:Proton glutamate symport protein
Family:Proton glutamate symport protein
Confidence and coverage
Confidence:100.0% Coverage: 85%
394 residues ( 85% 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  MNFPLIANIVVFVVLLFALAQTRHKQWSLAKKVLVGLVMGVVFGLALHTIYGSDSQVLKD
Secondary structure 


















SS confidence 



























































Disorder  ???

















??????























?????



Disorder confidence 



























































 
   .........70.........80.........90.........100.........110.........120
Sequence  SVQWFNIVGNGYVQLLQMIVMPLVFASILSAVARLHNASQLGKISFLTIGTLLFTTLIAA
Secondary structure 




SS confidence 



























































Disorder 































???????




















Disorder confidence 



























































 
   .........130.........140.........150.........160.........170.........180
Sequence  LVGVLVTNLFGLTAEGLVQGGAETARLNAIESNYVGKVSDLSVPQLVLSFIPKNPFADLT
Secondary structure 































SS confidence 



























































Disorder 











?????????????????????????????


















Disorder confidence 



























































 
   .........190.........200.........210.........220.........230.........240
Sequence  GANPTSIISVVIFAAFLGVAALKLLKDDAPKGERVLAAIDTLQSWVMKLVRLVMQLTPYG
Secondary structure 











SS confidence 



























































Disorder  ???



















???????





























Disorder confidence 



























































 
   .........250.........260.........270.........280.........290.........300
Sequence  VLALMTKVVAGSNLQDIIKLGSFVVASYLGLLIMFAVHGILLGINGVSPLKYFRKVWPVL
Secondary structure 





SS confidence 



























































Disorder 










?















































Disorder confidence 



























































 
   .........310.........320.........330.........340.........350.........360
Sequence  TFAFTSRSSAASIPLNVEAQTRRLGVPESIASFAASFGATIGQNGCAGLYPAMLAVMVAP
Secondary structure 








SS confidence 



























































Disorder 



























































Disorder confidence 



























































 
   .........370.........380.........390.........400.........410.........420
Sequence  TVGINPLDPMWIATLVGIVTVSSAGVAGVGGGATFAALIVLPAMGLPVTLVALLISVEPL
Secondary structure 

















SS confidence 



























































Disorder 






















??????













???













Disorder confidence 



























































 
   .........430.........440.........450.........460...
Sequence  IDMGRTALNVSGSMTAGTLTSQWLKQTDKAILDSEDDAELAHH
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 2nww chain A domain 1

3D model

Region: 29 - 444
Aligned: 394
Modelled: 416
Confidence: 100.0%
Identity: 30%
Fold: Proton glutamate symport protein
Superfamily: Proton glutamate symport protein
Family: Proton glutamate symport protein

Phyre2

PDB 3qnq chain D

3D model

Region: 444 - 463
Aligned: 20
Modelled: 20
Confidence: 54.9%
Identity: 30%
PDB header:membrane protein, transport protein
Chain: D: PDB Molecule:pts system, cellobiose-specific iic component;
PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system

Phyre2

PDB 1a77 chain A domain 1

3D model

Region: 367 - 405
Aligned: 38
Modelled: 39
Confidence: 18.8%
Identity: 11%
Fold: SAM domain-like
Superfamily: 5' to 3' exonuclease, C-terminal subdomain
Family: 5' to 3' exonuclease, C-terminal subdomain

Phyre2

PDB 2yvx chain D

3D model

Region: 21 - 85
Aligned: 65
Modelled: 65
Confidence: 16.1%
Identity: 20%
PDB header:transport protein
Chain: D: PDB Molecule:mg2+ transporter mgte;
PDBTitle: crystal structure of magnesium transporter mgte

Phyre2

PDB 1x0l chain B

3D model

Region: 390 - 449
Aligned: 60
Modelled: 60
Confidence: 14.4%
Identity: 15%
PDB header:oxidoreductase
Chain: B: PDB Molecule:homoisocitrate dehydrogenase;
PDBTitle: crystal structure of tetrameric homoisocitrate dehydrogenase from an2 extreme thermophile, thermus thermophilus

Phyre2

PDB 1o26 chain A

3D model

Region: 323 - 343
Aligned: 21
Modelled: 21
Confidence: 13.4%
Identity: 19%
Fold: Thymidylate synthase-complementing protein Thy1
Superfamily: Thymidylate synthase-complementing protein Thy1
Family: Thymidylate synthase-complementing protein Thy1

Phyre2

PDB 3ah5 chain E

3D model

Region: 322 - 343
Aligned: 22
Modelled: 22
Confidence: 13.0%
Identity: 9%
PDB header:transferase
Chain: E: PDB Molecule:thymidylate synthase thyx;
PDBTitle: crystal structure of flavin dependent thymidylate synthase thyx from2 helicobacter pylori complexed with fad and dump

Phyre2

PDB 3blx chain M

3D model

Region: 390 - 448
Aligned: 59
Modelled: 59
Confidence: 8.7%
Identity: 17%
PDB header:oxidoreductase
Chain: M: PDB Molecule:isocitrate dehydrogenase [nad] subunit 1;
PDBTitle: yeast isocitrate dehydrogenase (apo form)

Phyre2

PDB 1ul1 chain X domain 1

3D model

Region: 367 - 405
Aligned: 37
Modelled: 39
Confidence: 8.2%
Identity: 14%
Fold: SAM domain-like
Superfamily: 5' to 3' exonuclease, C-terminal subdomain
Family: 5' to 3' exonuclease, C-terminal subdomain

Phyre2

PDB 1rxw chain A domain 1

3D model

Region: 367 - 405
Aligned: 37
Modelled: 39
Confidence: 7.9%
Identity: 22%
Fold: SAM domain-like
Superfamily: 5' to 3' exonuclease, C-terminal subdomain
Family: 5' to 3' exonuclease, C-terminal subdomain

Phyre2

PDB 2cfa chain B

3D model

Region: 323 - 339
Aligned: 17
Modelled: 17
Confidence: 7.2%
Identity: 18%
PDB header:transferase
Chain: B: PDB Molecule:thymidylate synthase;
PDBTitle: structure of viral flavin-dependant thymidylate synthase2 thyx

Phyre2

PDB 1mc8 chain A domain 1

3D model

Region: 367 - 405
Aligned: 38
Modelled: 39
Confidence: 7.1%
Identity: 18%
Fold: SAM domain-like
Superfamily: 5' to 3' exonuclease, C-terminal subdomain
Family: 5' to 3' exonuclease, C-terminal subdomain

Phyre2

PDB 2pxr chain C domain 1

3D model

Region: 405 - 454
Aligned: 50
Modelled: 50
Confidence: 7.0%
Identity: 16%
Fold: Retrovirus capsid protein, N-terminal core domain
Superfamily: Retrovirus capsid protein, N-terminal core domain
Family: Retrovirus capsid protein, N-terminal core domain

Phyre2

PDB 1m9d chain C

3D model

Region: 405 - 454
Aligned: 50
Modelled: 50
Confidence: 6.9%
Identity: 16%
Fold: Retrovirus capsid protein, N-terminal core domain
Superfamily: Retrovirus capsid protein, N-terminal core domain
Family: Retrovirus capsid protein, N-terminal core domain

Phyre2

PDB 1m9f chain D

3D model

Region: 405 - 454
Aligned: 50
Modelled: 50
Confidence: 6.5%
Identity: 16%
Fold: Retrovirus capsid protein, N-terminal core domain
Superfamily: Retrovirus capsid protein, N-terminal core domain
Family: Retrovirus capsid protein, N-terminal core domain

Phyre2

PDB 1vf5 chain E

3D model

Region: 31 - 48
Aligned: 18
Modelled: 18
Confidence: 6.4%
Identity: 22%
PDB header:photosynthesis
Chain: E: PDB Molecule:protein pet l;
PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus

Phyre2

PDB 2e75 chain E

3D model

Region: 31 - 48
Aligned: 18
Modelled: 18
Confidence: 6.4%
Identity: 22%
PDB header:photosynthesis
Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6;
PDBTitle: crystal structure of the cytochrome b6f complex with 2-nonyl-4-2 hydroxyquinoline n-oxide (nqno) from m.laminosus

Phyre2

PDB 1vf5 chain R

3D model

Region: 31 - 48
Aligned: 18
Modelled: 18
Confidence: 6.4%
Identity: 22%
PDB header:photosynthesis
Chain: R: PDB Molecule:protein pet l;
PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus

Phyre2

PDB 2e76 chain E

3D model

Region: 31 - 48
Aligned: 18
Modelled: 18
Confidence: 6.4%
Identity: 22%
PDB header:photosynthesis
Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6;
PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus

Phyre2

PDB 2e74 chain E

3D model

Region: 31 - 48
Aligned: 18
Modelled: 18
Confidence: 6.4%
Identity: 22%
PDB header:photosynthesis
Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6;
PDBTitle: crystal structure of the cytochrome b6f complex from m.laminosus

Phyre2
1

d2nwwa1
2

c3qnqD_
3

d1a77a1
4

c2yvxD_
5

c1x0lB_
6

d1o26a_
7

c3ah5E_
8

c3blxM_
9

d1ul1x1
10

d1rxwa1
11

c2cfaB_
12

d1mc8a1
13

d2pxrc1
14

d1m9dc_
15

d1m9fd_
16

c1vf5E_
17

c2e75E_
18

c1vf5R_
19

c2e76E_
20

c2e74E_
21



22



23



24



25



26



27



28






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d2nwwa1



100.0 30 Fold:Proton glutamate symport protein
Superfamily:Proton glutamate symport protein
Family:Proton glutamate symport protein
2c3qnqD_



54.9 30 PDB header:membrane protein, transport protein
Chain: D: PDB Molecule:pts system, cellobiose-specific iic component;
PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system
3d1a77a1



18.8 11 Fold:SAM domain-like
Superfamily:5' to 3' exonuclease, C-terminal subdomain
Family:5' to 3' exonuclease, C-terminal subdomain
4c2yvxD_



16.1 20 PDB header:transport protein
Chain: D: PDB Molecule:mg2+ transporter mgte;
PDBTitle: crystal structure of magnesium transporter mgte
5c1x0lB_



14.4 15 PDB header:oxidoreductase
Chain: B: PDB Molecule:homoisocitrate dehydrogenase;
PDBTitle: crystal structure of tetrameric homoisocitrate dehydrogenase from an2 extreme thermophile, thermus thermophilus
6d1o26a_



13.4 19 Fold:Thymidylate synthase-complementing protein Thy1
Superfamily:Thymidylate synthase-complementing protein Thy1
Family:Thymidylate synthase-complementing protein Thy1
7c3ah5E_



13.0 9 PDB header:transferase
Chain: E: PDB Molecule:thymidylate synthase thyx;
PDBTitle: crystal structure of flavin dependent thymidylate synthase thyx from2 helicobacter pylori complexed with fad and dump
8c3blxM_



8.7 17 PDB header:oxidoreductase
Chain: M: PDB Molecule:isocitrate dehydrogenase [nad] subunit 1;
PDBTitle: yeast isocitrate dehydrogenase (apo form)
9d1ul1x1



8.2 14 Fold:SAM domain-like
Superfamily:5' to 3' exonuclease, C-terminal subdomain
Family:5' to 3' exonuclease, C-terminal subdomain
10d1rxwa1



7.9 22 Fold:SAM domain-like
Superfamily:5' to 3' exonuclease, C-terminal subdomain
Family:5' to 3' exonuclease, C-terminal subdomain
11c2cfaB_



7.2 18 PDB header:transferase
Chain: B: PDB Molecule:thymidylate synthase;
PDBTitle: structure of viral flavin-dependant thymidylate synthase2 thyx
12d1mc8a1



7.1 18 Fold:SAM domain-like
Superfamily:5' to 3' exonuclease, C-terminal subdomain
Family:5' to 3' exonuclease, C-terminal subdomain
13d2pxrc1



7.0 16 Fold:Retrovirus capsid protein, N-terminal core domain
Superfamily:Retrovirus capsid protein, N-terminal core domain
Family:Retrovirus capsid protein, N-terminal core domain
14d1m9dc_



6.9 16 Fold:Retrovirus capsid protein, N-terminal core domain
Superfamily:Retrovirus capsid protein, N-terminal core domain
Family:Retrovirus capsid protein, N-terminal core domain
15d1m9fd_



6.5 16 Fold:Retrovirus capsid protein, N-terminal core domain
Superfamily:Retrovirus capsid protein, N-terminal core domain
Family:Retrovirus capsid protein, N-terminal core domain
16c1vf5E_



6.4 22 PDB header:photosynthesis
Chain: E: PDB Molecule:protein pet l;
PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus
17c2e75E_



6.4 22 PDB header:photosynthesis
Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6;
PDBTitle: crystal structure of the cytochrome b6f complex with 2-nonyl-4-2 hydroxyquinoline n-oxide (nqno) from m.laminosus
18c1vf5R_



6.4 22 PDB header:photosynthesis
Chain: R: PDB Molecule:protein pet l;
PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus
19c2e76E_



6.4 22 PDB header:photosynthesis
Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6;
PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus
20c2e74E_



6.4 22 PDB header:photosynthesis
Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6;
PDBTitle: crystal structure of the cytochrome b6f complex from m.laminosus
21d2e74e1



not modelled 6.4 22 Fold:Single transmembrane helix
Superfamily:PetL subunit of the cytochrome b6f complex
Family:PetL subunit of the cytochrome b6f complex
22c2wlvA_



not modelled 6.3 16 PDB header:virus protein
Chain: A: PDB Molecule:gag polyprotein;
PDBTitle: structure of the n-terminal capsid domain of hiv-2
23c2jwaA_



not modelled 6.2 38 PDB header:transferase
Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2;
PDBTitle: erbb2 transmembrane segment dimer spatial structure
24d1b43a1



not modelled 6.1 18 Fold:SAM domain-like
Superfamily:5' to 3' exonuclease, C-terminal subdomain
Family:5' to 3' exonuclease, C-terminal subdomain
25d1hqsa_



not modelled 6.1 12 Fold:Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like
Family:Dimeric isocitrate & isopropylmalate dehydrogenases
26d1xo1a1



not modelled 6.1 18 Fold:SAM domain-like
Superfamily:5' to 3' exonuclease, C-terminal subdomain
Family:5' to 3' exonuclease, C-terminal subdomain
27d1ku2a1



not modelled 5.9 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma3 domain
28d1uxca_



not modelled 5.8 24 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator

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