Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP52600
DateThu Jan 5 12:05:50 GMT 2012
Unique Job IDf3d66b128fa44656

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1pw4a_
Top template information
Fold:MFS general substrate transporter
Superfamily:MFS general substrate transporter
Family:Glycerol-3-phosphate transporter
Confidence and coverage
Confidence:100.0% Coverage: 80%
408 residues ( 80% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
469 residues ( 92%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

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



















SS confidence 



























































Disorder  ??????????????
































???









Disorder confidence 



























































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


SS confidence 



























































Disorder 



























































Disorder confidence 



























































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





SS confidence 



























































Disorder 












?













































Disorder confidence 



























































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




















SS confidence 



























































Disorder 















??????





































Disorder confidence 



























































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












SS confidence 



























































Disorder 





















?





?





























Disorder confidence 



























































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










SS confidence 



























































Disorder 

























































?
Disorder confidence 



























































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









SS confidence 



























































Disorder 






























????


???


















Disorder confidence 



























































 
   .........430.........440.........450.........460.........470.........480
Sequence  TMTLWGRRESLHHSQLTATIDQFNPVFNSSSQIMDKYYGSLSGVLNEINNEITQQSLSIS
Secondary structure 













SS confidence 



























































Disorder 













?????????










??????????















Disorder confidence 



























































 
   .........490.........500.........510..
Sequence  ANEIFRMAAIAFILLTVLVWFAKPPFTAKGVG
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 1pw4 chain A

3D model

Region: 3 - 509
Aligned: 408
Modelled: 409
Confidence: 100.0%
Identity: 13%
Fold: MFS general substrate transporter
Superfamily: MFS general substrate transporter
Family: Glycerol-3-phosphate transporter

Phyre2

PDB 2gfp chain A

3D model

Region: 19 - 431
Aligned: 356
Modelled: 358
Confidence: 100.0%
Identity: 16%
PDB header:membrane protein
Chain: A: PDB Molecule:multidrug resistance protein d;
PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli

Phyre2

PDB 3o7p chain A

3D model

Region: 15 - 504
Aligned: 406
Modelled: 416
Confidence: 100.0%
Identity: 9%
PDB header:transport protein
Chain: A: PDB Molecule:l-fucose-proton symporter;
PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a)

Phyre2

PDB 2xut chain C

3D model

Region: 21 - 498
Aligned: 435
Modelled: 435
Confidence: 100.0%
Identity: 14%
PDB header:transport protein
Chain: C: PDB Molecule:proton/peptide symporter family protein;
PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter.

Phyre2

PDB 1pv7 chain A

3D model

Region: 16 - 508
Aligned: 399
Modelled: 403
Confidence: 100.0%
Identity: 12%
Fold: MFS general substrate transporter
Superfamily: MFS general substrate transporter
Family: LacY-like proton/sugar symporter

Phyre2

PDB 2g9p chain A

3D model

Region: 72 - 85
Aligned: 14
Modelled: 14
Confidence: 17.9%
Identity: 21%
PDB header:antimicrobial protein
Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a;
PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom

Phyre2

PDB 3b9y chain A

3D model

Region: 20 - 243
Aligned: 216
Modelled: 224
Confidence: 10.0%
Identity: 11%
PDB header:transport protein
Chain: A: PDB Molecule:ammonium transporter family rh-like protein;
PDBTitle: crystal structure of the nitrosomonas europaea rh protein

Phyre2

PDB 1wrg chain A

3D model

Region: 464 - 510
Aligned: 46
Modelled: 47
Confidence: 7.9%
Identity: 15%
PDB header:membrane protein
Chain: A: PDB Molecule:light-harvesting protein b-880, beta chain;
PDBTitle: light-harvesting complex 1 beta subunit from wild-type2 rhodospirillum rubrum

Phyre2

PDB 1fft chain B domain 2

3D model

Region: 463 - 511
Aligned: 49
Modelled: 49
Confidence: 7.6%
Identity: 14%
Fold: Transmembrane helix hairpin
Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region
Family: Cytochrome c oxidase subunit II-like, transmembrane region

Phyre2

PDB 3kzi chain T

3D model

Region: 484 - 507
Aligned: 24
Modelled: 24
Confidence: 7.3%
Identity: 17%
PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii

Phyre2

PDB 2axt chain T domain 1

3D model

Region: 484 - 507
Aligned: 24
Modelled: 24
Confidence: 7.3%
Identity: 17%
Fold: Single transmembrane helix
Superfamily: Photosystem II reaction center protein T, PsbT
Family: PsbT-like

Phyre2

PDB 2axt chain T

3D model

Region: 484 - 507
Aligned: 24
Modelled: 24
Confidence: 7.3%
Identity: 17%
PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center t protein;
PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus

Phyre2

PDB 3a0b chain T

3D model

Region: 484 - 507
Aligned: 24
Modelled: 24
Confidence: 7.3%
Identity: 17%
PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of br-substituted photosystem ii complex

Phyre2

PDB 3a0h chain T

3D model

Region: 484 - 507
Aligned: 24
Modelled: 24
Confidence: 7.3%
Identity: 17%
PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of i-substituted photosystem ii complex

Phyre2

PDB 3arc chain T

3D model

Region: 484 - 507
Aligned: 24
Modelled: 24
Confidence: 7.3%
Identity: 17%
PDB header:electron transport, photosynthesis
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution

Phyre2

PDB 2axt chain T

3D model

Region: 484 - 507
Aligned: 24
Modelled: 24
Confidence: 7.3%
Identity: 17%
PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center t protein;
PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus

Phyre2

PDB 3a0h chain T

3D model

Region: 484 - 507
Aligned: 24
Modelled: 24
Confidence: 7.3%
Identity: 17%
PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of i-substituted photosystem ii complex

Phyre2

PDB 1s5l chain T

3D model

Region: 484 - 507
Aligned: 24
Modelled: 24
Confidence: 7.3%
Identity: 17%
PDB header:photosynthesis
Chain: T: PDB Molecule:photosystem ii psbt protein;
PDBTitle: architecture of the photosynthetic oxygen evolving center

Phyre2

PDB 1s5l chain T

3D model

Region: 484 - 507
Aligned: 24
Modelled: 24
Confidence: 7.3%
Identity: 17%
PDB header:photosynthesis
Chain: T: PDB Molecule:photosystem ii psbt protein;
PDBTitle: architecture of the photosynthetic oxygen evolving center

Phyre2

PDB 3bz1 chain T

3D model

Region: 484 - 507
Aligned: 24
Modelled: 24
Confidence: 7.2%
Identity: 17%
PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer

Phyre2
1

d1pw4a_
2

c2gfpA_
3

c3o7pA_
4

c2xutC_
5

d1pv7a_
6

c2g9pA_
7

c3b9yA_
8

c1wrgA_
9

d1fftb2
10

c3kziT_
11

d2axtt1
12

c2axtT_
13

c3a0bt_
14

c3a0hT_
15

c3arcT_
16

c2axtt_
17

c3a0ht_
18

c1s5lt_
19

c1s5lT_
20

c3bz1T_
21



22



23






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1pw4a_



100.0 13 Fold:MFS general substrate transporter
Superfamily:MFS general substrate transporter
Family:Glycerol-3-phosphate transporter
2c2gfpA_



100.0 16 PDB header:membrane protein
Chain: A: PDB Molecule:multidrug resistance protein d;
PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli
3c3o7pA_



100.0 9 PDB header:transport protein
Chain: A: PDB Molecule:l-fucose-proton symporter;
PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a)
4c2xutC_



100.0 14 PDB header:transport protein
Chain: C: PDB Molecule:proton/peptide symporter family protein;
PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter.
5d1pv7a_



100.0 12 Fold:MFS general substrate transporter
Superfamily:MFS general substrate transporter
Family:LacY-like proton/sugar symporter
6c2g9pA_



17.9 21 PDB header:antimicrobial protein
Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a;
PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom
7c3b9yA_



10.0 11 PDB header:transport protein
Chain: A: PDB Molecule:ammonium transporter family rh-like protein;
PDBTitle: crystal structure of the nitrosomonas europaea rh protein
8c1wrgA_



7.9 15 PDB header:membrane protein
Chain: A: PDB Molecule:light-harvesting protein b-880, beta chain;
PDBTitle: light-harvesting complex 1 beta subunit from wild-type2 rhodospirillum rubrum
9d1fftb2



7.6 14 Fold:Transmembrane helix hairpin
Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region
Family:Cytochrome c oxidase subunit II-like, transmembrane region
10c3kziT_



7.3 17 PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii
11d2axtt1



7.3 17 Fold:Single transmembrane helix
Superfamily:Photosystem II reaction center protein T, PsbT
Family:PsbT-like
12c2axtT_



7.3 17 PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center t protein;
PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus
13c3a0bt_



7.3 17 PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of br-substituted photosystem ii complex
14c3a0hT_



7.3 17 PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of i-substituted photosystem ii complex
15c3arcT_



7.3 17 PDB header:electron transport, photosynthesis
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution
16c2axtt_



7.3 17 PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center t protein;
PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus
17c3a0ht_



7.3 17 PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of i-substituted photosystem ii complex
18c1s5lt_



7.3 17 PDB header:photosynthesis
Chain: T: PDB Molecule:photosystem ii psbt protein;
PDBTitle: architecture of the photosynthetic oxygen evolving center
19c1s5lT_



7.3 17 PDB header:photosynthesis
Chain: T: PDB Molecule:photosystem ii psbt protein;
PDBTitle: architecture of the photosynthetic oxygen evolving center
20c3bz1T_



7.2 17 PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer
21c3bz2T_



not modelled 7.2 17 PDB header:electron transport
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer
22c3prqT_



not modelled 7.2 17 PDB header:photosynthesis
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer
23c3prrT_



not modelled 7.2 17 PDB header:photosynthesis
Chain: T: PDB Molecule:photosystem ii reaction center protein t;
PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer

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