Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0ABV6
DateThu Jan 5 11:16:29 GMT 2012
Unique Job ID2aa7d57323bd2e09

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2pfuA_
Top template information
PDB header:transport protein
Chain: A: PDB Molecule:biopolymer transport exbd protein;
PDBTitle: nmr strcuture determination of the periplasmic domain of exbd from2 e.coli
Confidence and coverage
Confidence: 99.6% Coverage: 65%
93 residues ( 65% of your sequence) have been modelled with 99.6% 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.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MARARGRGRRDLKSEINIVPLLDVLLVLLLIFMATAPIITQSVEVDLPDATESQAVSSND
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Disorder  ???????????????





















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   .........70.........80.........90.........100.........110.........120
Sequence  NPPVIVEVSGIGQYTVVVEKDRLERLPPEQVVAEVSSRFKANPKTVFLIGGAKDVPYDEI
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   .........130.........140..
Sequence  IKALNLLHSAGVKSVGLMTQPI
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 2pfu chain A

3D model

Region: 42 - 141
Aligned: 93
Modelled: 100
Confidence: 99.6%
Identity: 22%
PDB header:transport protein
Chain: A: PDB Molecule:biopolymer transport exbd protein;
PDBTitle: nmr strcuture determination of the periplasmic domain of exbd from2 e.coli

Phyre2

PDB 2jwl chain B

3D model

Region: 61 - 133
Aligned: 73
Modelled: 73
Confidence: 99.4%
Identity: 51%
PDB header:membrane protein
Chain: B: PDB Molecule:protein tolr;
PDBTitle: solution structure of periplasmic domain of tolr from h.2 influenzae with saxs data

Phyre2

PDB 2e8a chain A domain 1

3D model

Region: 88 - 141
Aligned: 53
Modelled: 54
Confidence: 49.1%
Identity: 9%
Fold: Ribonuclease H-like motif
Superfamily: Actin-like ATPase domain
Family: Actin/HSP70

Phyre2

PDB 2axt chain K domain 1

3D model

Region: 16 - 31
Aligned: 16
Modelled: 16
Confidence: 45.0%
Identity: 25%
Fold: Single transmembrane helix
Superfamily: Photosystem II reaction center protein K, PsbK
Family: PsbK-like

Phyre2

PDB 1bup chain A domain 1

3D model

Region: 88 - 141
Aligned: 53
Modelled: 54
Confidence: 40.6%
Identity: 8%
Fold: Ribonuclease H-like motif
Superfamily: Actin-like ATPase domain
Family: Actin/HSP70

Phyre2

PDB 3a0b chain K

3D model

Region: 16 - 31
Aligned: 16
Modelled: 16
Confidence: 40.4%
Identity: 25%
PDB header:electron transport
Chain: K: PDB Molecule:photosystem ii reaction center protein k;
PDBTitle: crystal structure of br-substituted photosystem ii complex

Phyre2

PDB 1jce chain A domain 1

3D model

Region: 88 - 141
Aligned: 54
Modelled: 54
Confidence: 38.0%
Identity: 22%
Fold: Ribonuclease H-like motif
Superfamily: Actin-like ATPase domain
Family: Actin/HSP70

Phyre2

PDB 2jvf chain A

3D model

Region: 61 - 140
Aligned: 80
Modelled: 80
Confidence: 34.0%
Identity: 13%
PDB header:de novo protein
Chain: A: PDB Molecule:de novo protein m7;
PDBTitle: solution structure of m7, a computationally-designed2 artificial protein

Phyre2

PDB 1qys chain A

3D model

Region: 63 - 140
Aligned: 77
Modelled: 78
Confidence: 33.1%
Identity: 12%
PDB header:de novo protein
Chain: A: PDB Molecule:top7;
PDBTitle: crystal structure of top7: a computationally designed2 protein with a novel fold

Phyre2

PDB 3a0b chain K

3D model

Region: 16 - 31
Aligned: 16
Modelled: 16
Confidence: 30.6%
Identity: 25%
PDB header:electron transport
Chain: K: PDB Molecule:photosystem ii reaction center protein k;
PDBTitle: crystal structure of br-substituted photosystem ii complex

Phyre2

PDB 3a0h chain K

3D model

Region: 16 - 31
Aligned: 16
Modelled: 16
Confidence: 24.1%
Identity: 25%
PDB header:electron transport
Chain: K: PDB Molecule:photosystem ii reaction center protein k;
PDBTitle: crystal structure of i-substituted photosystem ii complex

Phyre2

PDB 3bma chain C

3D model

Region: 112 - 142
Aligned: 30
Modelled: 31
Confidence: 22.5%
Identity: 17%
PDB header:ligase
Chain: C: PDB Molecule:d-alanyl-lipoteichoic acid synthetase;
PDBTitle: crystal structure of d-alanyl-lipoteichoic acid synthetase from2 streptococcus pneumoniae r6

Phyre2

PDB 1f75 chain A

3D model

Region: 117 - 137
Aligned: 21
Modelled: 21
Confidence: 21.3%
Identity: 24%
Fold: Undecaprenyl diphosphate synthase
Superfamily: Undecaprenyl diphosphate synthase
Family: Undecaprenyl diphosphate synthase

Phyre2

PDB 1dkg chain D domain 1

3D model

Region: 88 - 141
Aligned: 53
Modelled: 54
Confidence: 21.1%
Identity: 9%
Fold: Ribonuclease H-like motif
Superfamily: Actin-like ATPase domain
Family: Actin/HSP70

Phyre2

PDB 1qyi chain A

3D model

Region: 115 - 139
Aligned: 24
Modelled: 25
Confidence: 20.9%
Identity: 42%
Fold: HAD-like
Superfamily: HAD-like
Family: Hypothetical protein MW1667 (SA1546)

Phyre2

PDB 2d0o chain A domain 1

3D model

Region: 97 - 140
Aligned: 44
Modelled: 44
Confidence: 19.9%
Identity: 14%
Fold: The "swivelling" beta/beta/alpha domain
Superfamily: Swiveling domain of dehydratase reactivase alpha subunit
Family: Swiveling domain of dehydratase reactivase alpha subunit

Phyre2

PDB 2vfw chain B

3D model

Region: 117 - 137
Aligned: 21
Modelled: 21
Confidence: 18.0%
Identity: 24%
PDB header:transferase
Chain: B: PDB Molecule:short-chain z-isoprenyl diphosphate synthetase;
PDBTitle: rv1086 native

Phyre2

PDB 1jp3 chain A

3D model

Region: 117 - 137
Aligned: 21
Modelled: 21
Confidence: 17.9%
Identity: 14%
PDB header:transferase
Chain: A: PDB Molecule:undecaprenyl pyrophosphate synthase;
PDBTitle: structure of e.coli undecaprenyl pyrophosphate synthase

Phyre2

PDB 1g8f chain A domain 3

3D model

Region: 100 - 132
Aligned: 33
Modelled: 33
Confidence: 17.8%
Identity: 12%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: ATP sulfurylase C-terminal domain

Phyre2

PDB 3qm3 chain C

3D model

Region: 90 - 140
Aligned: 47
Modelled: 51
Confidence: 17.8%
Identity: 19%
PDB header:lyase
Chain: C: PDB Molecule:fructose-bisphosphate aldolase;
PDBTitle: 1.85 angstrom resolution crystal structure of fructose-bisphosphate2 aldolase (fba) from campylobacter jejuni

Phyre2
1

c2pfuA_
2

c2jwlB_
3

d2e8aa1
4

d2axtk1
5

d1bupa1
6

c3a0bK_
7

d1jcea1
8

c2jvfA_
9

c1qysA_
10

c3a0bk_
11

c3a0hk_
12

c3bmaC_
13

d1f75a_
14

d1dkgd1
15

d1qyia_
16

d2d0oa1
17

c2vfwB_
18

c1jp3A_
19

d1g8fa3
20

c3qm3C_
21



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24



25



26



27



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29



30



31



32



33



34



35



36



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38



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42



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44



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48



49



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51



52



53



54



55






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2pfuA_



99.6 22 PDB header:transport protein
Chain: A: PDB Molecule:biopolymer transport exbd protein;
PDBTitle: nmr strcuture determination of the periplasmic domain of exbd from2 e.coli
2c2jwlB_



99.4 51 PDB header:membrane protein
Chain: B: PDB Molecule:protein tolr;
PDBTitle: solution structure of periplasmic domain of tolr from h.2 influenzae with saxs data
3d2e8aa1



49.1 9 Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:Actin/HSP70
4d2axtk1



45.0 25 Fold:Single transmembrane helix
Superfamily:Photosystem II reaction center protein K, PsbK
Family:PsbK-like
5d1bupa1



40.6 8 Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:Actin/HSP70
6c3a0bK_



40.4 25 PDB header:electron transport
Chain: K: PDB Molecule:photosystem ii reaction center protein k;
PDBTitle: crystal structure of br-substituted photosystem ii complex
7d1jcea1



38.0 22 Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:Actin/HSP70
8c2jvfA_



34.0 13 PDB header:de novo protein
Chain: A: PDB Molecule:de novo protein m7;
PDBTitle: solution structure of m7, a computationally-designed2 artificial protein
9c1qysA_



33.1 12 PDB header:de novo protein
Chain: A: PDB Molecule:top7;
PDBTitle: crystal structure of top7: a computationally designed2 protein with a novel fold
10c3a0bk_



30.6 25 PDB header:electron transport
Chain: K: PDB Molecule:photosystem ii reaction center protein k;
PDBTitle: crystal structure of br-substituted photosystem ii complex
11c3a0hk_



24.1 25 PDB header:electron transport
Chain: K: PDB Molecule:photosystem ii reaction center protein k;
PDBTitle: crystal structure of i-substituted photosystem ii complex
12c3bmaC_



22.5 17 PDB header:ligase
Chain: C: PDB Molecule:d-alanyl-lipoteichoic acid synthetase;
PDBTitle: crystal structure of d-alanyl-lipoteichoic acid synthetase from2 streptococcus pneumoniae r6
13d1f75a_



21.3 24 Fold:Undecaprenyl diphosphate synthase
Superfamily:Undecaprenyl diphosphate synthase
Family:Undecaprenyl diphosphate synthase
14d1dkgd1



21.1 9 Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:Actin/HSP70
15d1qyia_



20.9 42 Fold:HAD-like
Superfamily:HAD-like
Family:Hypothetical protein MW1667 (SA1546)
16d2d0oa1



19.9 14 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:Swiveling domain of dehydratase reactivase alpha subunit
Family:Swiveling domain of dehydratase reactivase alpha subunit
17c2vfwB_



18.0 24 PDB header:transferase
Chain: B: PDB Molecule:short-chain z-isoprenyl diphosphate synthetase;
PDBTitle: rv1086 native
18c1jp3A_



17.9 14 PDB header:transferase
Chain: A: PDB Molecule:undecaprenyl pyrophosphate synthase;
PDBTitle: structure of e.coli undecaprenyl pyrophosphate synthase
19d1g8fa3



17.8 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:ATP sulfurylase C-terminal domain
20c3qm3C_



17.8 19 PDB header:lyase
Chain: C: PDB Molecule:fructose-bisphosphate aldolase;
PDBTitle: 1.85 angstrom resolution crystal structure of fructose-bisphosphate2 aldolase (fba) from campylobacter jejuni
21c3pm6B_



not modelled 17.5 13 PDB header:lyase
Chain: B: PDB Molecule:putative fructose-bisphosphate aldolase;
PDBTitle: crystal structure of a putative fructose-1,6-biphosphate aldolase from2 coccidioides immitis solved by combined sad mr
22c3muxB_



not modelled 17.1 18 PDB header:lyase
Chain: B: PDB Molecule:putative 4-hydroxy-2-oxoglutarate aldolase;
PDBTitle: the crystal structure of a putative 4-hydroxy-2-oxoglutarate aldolase2 from bacillus anthracis to 1.45a
23c3m6yA_



not modelled 15.9 16 PDB header:lyase
Chain: A: PDB Molecule:4-hydroxy-2-oxoglutarate aldolase;
PDBTitle: structure of 4-hydroxy-2-oxoglutarate aldolase from bacillus cereus at2 1.45 a resolution.
24d1ueha_



not modelled 15.7 14 Fold:Undecaprenyl diphosphate synthase
Superfamily:Undecaprenyl diphosphate synthase
Family:Undecaprenyl diphosphate synthase
25c2d2rA_



not modelled 15.3 5 PDB header:transferase
Chain: A: PDB Molecule:undecaprenyl pyrophosphate synthase;
PDBTitle: crystal structure of helicobacter pylori undecaprenyl pyrophosphate2 synthase
26c3m0zD_



not modelled 14.0 20 PDB header:lyase
Chain: D: PDB Molecule:putative aldolase;
PDBTitle: crystal structure of putative aldolase from klebsiella2 pneumoniae.
27d1gvfa_



not modelled 13.6 28 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class II FBP aldolase
28d1olta_



not modelled 13.2 13 Fold:TIM beta/alpha-barrel
Superfamily:Radical SAM enzymes
Family:Oxygen-independent coproporphyrinogen III oxidase HemN
29c3bz1y_



not modelled 12.5 0 PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii protein y;
PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer
30c3a0hy_



not modelled 12.5 0 PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12;
PDBTitle: crystal structure of i-substituted photosystem ii complex
31c3a0hY_



not modelled 12.5 0 PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12;
PDBTitle: crystal structure of i-substituted photosystem ii complex
32c3arcy_



not modelled 12.1 0 PDB header:electron transport, photosynthesis
Chain: Y: PDB Molecule:protein ycf12;
PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution
33c3arcY_



not modelled 12.1 0 PDB header:electron transport, photosynthesis
Chain: Y: PDB Molecule:protein ycf12;
PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution
34c3a0by_



not modelled 11.8 0 PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12;
PDBTitle: crystal structure of br-substituted photosystem ii complex
35c3gmgB_



not modelled 11.1 22 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein rv1825/mt1873;
PDBTitle: crystal structure of an uncharacterized conserved protein2 from mycobacterium tuberculosis
36d1xr4a1



not modelled 10.8 13 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:CoA transferase alpha subunit-like
37d2ohwa1



not modelled 9.6 15 Fold:Bacillus chorismate mutase-like
Superfamily:YueI-like
Family:YueI-like
38c3gk0H_



not modelled 9.5 14 PDB header:transferase
Chain: H: PDB Molecule:pyridoxine 5'-phosphate synthase;
PDBTitle: crystal structure of pyridoxal phosphate biosynthetic2 protein from burkholderia pseudomallei
39c3a0bY_



not modelled 9.4 0 PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12;
PDBTitle: crystal structure of br-substituted photosystem ii complex
40c3ivuB_



not modelled 9.0 10 PDB header:transferase
Chain: B: PDB Molecule:homocitrate synthase, mitochondrial;
PDBTitle: homocitrate synthase lys4 bound to 2-og
41d1a9xa4



not modelled 8.8 15 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
42d1rvga_



not modelled 8.2 23 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class II FBP aldolase
43c3iprC_



not modelled 8.1 13 PDB header:transferase
Chain: C: PDB Molecule:pts system, iia component;
PDBTitle: crystal structure of the enterococcus faecalis gluconate2 specific eiia phosphotransferase system component
44d1b0aa2



not modelled 8.1 11 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Tetrahydrofolate dehydrogenase/cyclohydrolase
45d2gycm1



not modelled 8.0 12 Fold:Ribonuclease H-like motif
Superfamily:Translational machinery components
Family:Ribosomal protein L18 and S11
46d1nvma2



not modelled 7.8 11 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:HMGL-like
47d1zhva2



not modelled 7.6 32 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:Atu0741-like
48c3q94B_



not modelled 7.6 19 PDB header:lyase
Chain: B: PDB Molecule:fructose-bisphosphate aldolase, class ii;
PDBTitle: the crystal structure of fructose 1,6-bisphosphate aldolase from2 bacillus anthracis str. 'ames ancestor'
49d1edza2



not modelled 7.6 15 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Tetrahydrofolate dehydrogenase/cyclohydrolase
50c2vg2C_



not modelled 6.9 19 PDB header:transferase
Chain: C: PDB Molecule:undecaprenyl pyrophosphate synthetase;
PDBTitle: rv2361 with ipp
51d1ovya_



not modelled 6.5 11 Fold:Ribonuclease H-like motif
Superfamily:Translational machinery components
Family:Ribosomal protein L18 and S11
52c2bdqA_



not modelled 6.5 15 PDB header:metal transport
Chain: A: PDB Molecule:copper homeostasis protein cutc;
PDBTitle: crystal structure of the putative copper homeostasis2 protein cutc from streptococcus agalactiae, northeast3 strucural genomics target sar15.
53d1a4ia2



not modelled 6.3 20 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Tetrahydrofolate dehydrogenase/cyclohydrolase
54d1ujpa_



not modelled 5.7 30 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
55d1m5wa_



not modelled 5.1 13 Fold:TIM beta/alpha-barrel
Superfamily:Pyridoxine 5'-phosphate synthase
Family:Pyridoxine 5'-phosphate synthase

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