Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP52645
DateThu Jan 5 12:05:58 GMT 2012
Unique Job ID4de6e716f4db8da3

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1xmec1
Top template information
Fold:Single transmembrane helix
Superfamily:Bacterial ba3 type cytochrome c oxidase subunit IIa
Family:Bacterial ba3 type cytochrome c oxidase subunit IIa
Confidence and coverage
Confidence: 32.1% Coverage: 3%
23 residues ( 3% of your sequence) have been modelled with 32.1% 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.
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3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MLGKYKAVLALLLLIILVPLTLLMTLGLWVPTLAGIWLPLGTRIALDESPRITRKGLIIP
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   .........70.........80.........90.........100.........110.........120
Sequence  DLRYLVGDCQLAHITNASLSHPSRWLLNVGTVELDSACLAKLPQTEQSPAAPKTLAQWQA
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   .........130.........140.........150.........160.........170.........180
Sequence  MLPNTWINIDKLIFSPWQEWQGKLSLALTSDIQQLRYQGEKVKFQGQLKGQQLTVSELDV
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   .........190.........200.........210.........220.........230.........240
Sequence  VAFENQPPVKLVGEFAMPLVPDGLPVSGHATATLNLPQEPSLVDAELDWQENSGQLIVLA
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   .........250.........260.........270.........280.........290.........300
Sequence  RDNGDPLLDLPWQITRQQLTVSDGRWSWPYAGFPLSGRLGVKVDNWQAGLENALVSGRLS
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   .........310.........320.........330.........340.........350.........360
Sequence  VLTQGQAGKGNAVLNFGPGKLSMDNSQLPLQLTGEAKQADLILYARLPAQLSGSLSDPTL
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   .........370.........380.........390.........400.........410.........420
Sequence  TFEPGALLRSKGRVIDSLDIDEIRWPLAGVKVTQRGVDGRLQAILQAHENELGDFVLHMD
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   .........430.........440.........450.........460.........470.........480
Sequence  GLANDFLPDAGRWQWRYWGKGSFTPMNATWDVAGKGEWHDSTITLTDLSTGFDQLQYGTM
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   .........490.........500.........510.........520.........530.........540
Sequence  TVEKPRLILDKPIVWVRDAQHPSFSGALSLDAGQTLFTGGSVLPPSTLKFSVDGRDPTYF
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   .........550.........560.........570.........580.........590.........600
Sequence  LFKGDLHAGEIGPVRVNGRWDGIRLRGNAWWPKQSLTVFQPLVPPDWKMNLRDGELYAQV
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   .........610.........620.........630.........640.........650.........660
Sequence  AFSAAPEQGFRAGGHGVLKGGSAWMPDNQVNGVDFVLPFRFADGAWHLGTRGPVTLRIAE
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   .........670.........680.........690.........700.........710.........720
Sequence  VINLVTAKNITADLQGRYPWTEEEPLLLTDVSVDVLGGNVLMKQLRMPQHDPALLRLNNL
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   .........730.........740.........750.........760.........770.........780
Sequence  SSSELVSAVNPKQFAMSGAFSGALPLWLNNEKWIVKDGWLANSGPMTLRLDKDTADAVVK
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   .........790.........800.........810.........820.........830.........840
Sequence  DNMTAGSAINWLRYMEISRSSTKINLDNLGLLTMQANITGTSRVDGKSGTVNLNYHHEEN
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   .........850.........860.........870.........
Sequence  IFTLWRSLRFGDNLQAWLEQNARLPGNDCPQGKECEEKQ
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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 1xme chain C domain 1

3D model

Region: 4 - 26
Aligned: 23
Modelled: 23
Confidence: 32.1%
Identity: 30%
Fold: Single transmembrane helix
Superfamily: Bacterial ba3 type cytochrome c oxidase subunit IIa
Family: Bacterial ba3 type cytochrome c oxidase subunit IIa

Phyre2

PDB 1im3 chain D

3D model

Region: 746 - 764
Aligned: 19
Modelled: 19
Confidence: 29.1%
Identity: 16%
Fold: Immunoglobulin-like beta-sandwich
Superfamily: E set domains
Family: Cytomegalovirus protein US2

Phyre2

PDB 1e50 chain B

3D model

Region: 738 - 776
Aligned: 38
Modelled: 39
Confidence: 19.9%
Identity: 26%
Fold: Core binding factor beta, CBF
Superfamily: Core binding factor beta, CBF
Family: Core binding factor beta, CBF

Phyre2

PDB 3ghf chain A

3D model

Region: 820 - 849
Aligned: 30
Modelled: 30
Confidence: 19.9%
Identity: 17%
PDB header:cell cycle
Chain: A: PDB Molecule:septum site-determining protein minc;
PDBTitle: crystal structure of the septum site-determining protein2 minc from salmonella typhimurium

Phyre2

PDB 2isy chain A domain 2

3D model

Region: 850 - 874
Aligned: 24
Modelled: 25
Confidence: 18.5%
Identity: 17%
Fold: Iron-dependent repressor protein, dimerization domain
Superfamily: Iron-dependent repressor protein, dimerization domain
Family: Iron-dependent repressor protein, dimerization domain

Phyre2

PDB 2im5 chain C

3D model

Region: 767 - 817
Aligned: 51
Modelled: 51
Confidence: 18.0%
Identity: 18%
PDB header:transferase
Chain: C: PDB Molecule:nicotinate phosphoribosyltransferase;
PDBTitle: crystal structure of nicotinate phosphoribosyltransferase2 from porphyromonas gingivalis

Phyre2

PDB 2nwa chain A domain 1

3D model

Region: 827 - 844
Aligned: 18
Modelled: 15
Confidence: 16.4%
Identity: 44%
Fold: PUA domain-like
Superfamily: PUA domain-like
Family: YtmB-like

Phyre2

PDB 1gl4 chain A domain 1

3D model

Region: 793 - 833
Aligned: 39
Modelled: 41
Confidence: 14.6%
Identity: 18%
Fold: GFP-like
Superfamily: GFP-like
Family: Domain G2 of nidogen-1

Phyre2

PDB 1b26 chain A domain 2

3D model

Region: 743 - 811
Aligned: 69
Modelled: 69
Confidence: 11.8%
Identity: 13%
Fold: Aminoacid dehydrogenase-like, N-terminal domain
Superfamily: Aminoacid dehydrogenase-like, N-terminal domain
Family: Aminoacid dehydrogenases

Phyre2

PDB 2cg5 chain A

3D model

Region: 793 - 841
Aligned: 43
Modelled: 49
Confidence: 11.4%
Identity: 12%
PDB header:transferase/hydrolase
Chain: A: PDB Molecule:l-aminoadipate-semialdehyde dehydrogenase-
PDBTitle: structure of aminoadipate-semialdehyde dehydrogenase-2 phosphopantetheinyl transferase in complex with cytosolic3 acyl carrier protein and coenzyme a

Phyre2

PDB 3db3 chain A

3D model

Region: 824 - 839
Aligned: 16
Modelled: 16
Confidence: 11.2%
Identity: 25%
PDB header:ligase
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase uhrf1;
PDBTitle: crystal structure of the tandem tudor domains of the e3 ubiquitin-2 protein ligase uhrf1 in complex with trimethylated histone h3-k93 peptide

Phyre2

PDB 1h4u chain A

3D model

Region: 793 - 833
Aligned: 39
Modelled: 41
Confidence: 8.7%
Identity: 18%
PDB header:extracellular matrix protein
Chain: A: PDB Molecule:nidogen-1;
PDBTitle: domain g2 of mouse nidogen-1

Phyre2

PDB 1v9l chain A domain 2

3D model

Region: 743 - 811
Aligned: 69
Modelled: 69
Confidence: 8.3%
Identity: 14%
Fold: Aminoacid dehydrogenase-like, N-terminal domain
Superfamily: Aminoacid dehydrogenase-like, N-terminal domain
Family: Aminoacid dehydrogenases

Phyre2

PDB 1hwx chain A domain 2

3D model

Region: 743 - 811
Aligned: 69
Modelled: 69
Confidence: 8.1%
Identity: 14%
Fold: Aminoacid dehydrogenase-like, N-terminal domain
Superfamily: Aminoacid dehydrogenase-like, N-terminal domain
Family: Aminoacid dehydrogenases

Phyre2

PDB 1bgv chain A domain 2

3D model

Region: 743 - 811
Aligned: 69
Modelled: 69
Confidence: 8.0%
Identity: 16%
Fold: Aminoacid dehydrogenase-like, N-terminal domain
Superfamily: Aminoacid dehydrogenase-like, N-terminal domain
Family: Aminoacid dehydrogenases

Phyre2

PDB 1piq chain A

3D model

Region: 846 - 862
Aligned: 17
Modelled: 17
Confidence: 8.0%
Identity: 18%
PDB header:dna binding protein
Chain: A: PDB Molecule:protein (general control protein gcn4-piq);
PDBTitle: crystal structure of gcn4-piq, a trimeric coiled coil with buried2 polar residues

Phyre2

PDB 1jb0 chain J

3D model

Region: 18 - 40
Aligned: 23
Modelled: 23
Confidence: 7.3%
Identity: 17%
Fold: Single transmembrane helix
Superfamily: Subunit IX of photosystem I reaction centre, PsaJ
Family: Subunit IX of photosystem I reaction centre, PsaJ

Phyre2

PDB 2o01 chain J

3D model

Region: 18 - 40
Aligned: 23
Modelled: 23
Confidence: 7.3%
Identity: 17%
PDB header:photosynthesis
Chain: J: PDB Molecule:photosystem i reaction center subunit ix;
PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution

Phyre2

PDB 1euz chain A domain 2

3D model

Region: 743 - 811
Aligned: 69
Modelled: 69
Confidence: 7.1%
Identity: 13%
Fold: Aminoacid dehydrogenase-like, N-terminal domain
Superfamily: Aminoacid dehydrogenase-like, N-terminal domain
Family: Aminoacid dehydrogenases

Phyre2

PDB 1xo8 chain A

3D model

Region: 655 - 750
Aligned: 95
Modelled: 96
Confidence: 6.9%
Identity: 9%
Fold: Immunoglobulin-like beta-sandwich
Superfamily: LEA14-like
Family: LEA14-like

Phyre2
1

d1xmec1
2

d1im3d_
3

d1e50b_
4

c3ghfA_
5

d2isya2
6

c2im5C_
7

d2nwaa1
8

d1gl4a1
9

d1b26a2
10

c2cg5A_
11

c3db3A_
12

c1h4uA_
13

d1v9la2
14

d1hwxa2
15

d1bgva2
16

c1piqA_
17

d1jb0j_
18

c2o01J_
19

d1euza2
20

d1xo8a_
21



22



23



24



25



26



27



28



29



30



31



32



33



34



35



36



37



38



39



40



41



42



43






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1xmec1



32.1 30 Fold:Single transmembrane helix
Superfamily:Bacterial ba3 type cytochrome c oxidase subunit IIa
Family:Bacterial ba3 type cytochrome c oxidase subunit IIa
2d1im3d_



29.1 16 Fold:Immunoglobulin-like beta-sandwich
Superfamily:E set domains
Family:Cytomegalovirus protein US2
3d1e50b_



19.9 26 Fold:Core binding factor beta, CBF
Superfamily:Core binding factor beta, CBF
Family:Core binding factor beta, CBF
4c3ghfA_



19.9 17 PDB header:cell cycle
Chain: A: PDB Molecule:septum site-determining protein minc;
PDBTitle: crystal structure of the septum site-determining protein2 minc from salmonella typhimurium
5d2isya2



18.5 17 Fold:Iron-dependent repressor protein, dimerization domain
Superfamily:Iron-dependent repressor protein, dimerization domain
Family:Iron-dependent repressor protein, dimerization domain
6c2im5C_



18.0 18 PDB header:transferase
Chain: C: PDB Molecule:nicotinate phosphoribosyltransferase;
PDBTitle: crystal structure of nicotinate phosphoribosyltransferase2 from porphyromonas gingivalis
7d2nwaa1



16.4 44 Fold:PUA domain-like
Superfamily:PUA domain-like
Family:YtmB-like
8d1gl4a1



14.6 18 Fold:GFP-like
Superfamily:GFP-like
Family:Domain G2 of nidogen-1
9d1b26a2



11.8 13 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Aminoacid dehydrogenases
10c2cg5A_



11.4 12 PDB header:transferase/hydrolase
Chain: A: PDB Molecule:l-aminoadipate-semialdehyde dehydrogenase-
PDBTitle: structure of aminoadipate-semialdehyde dehydrogenase-2 phosphopantetheinyl transferase in complex with cytosolic3 acyl carrier protein and coenzyme a
11c3db3A_



11.2 25 PDB header:ligase
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase uhrf1;
PDBTitle: crystal structure of the tandem tudor domains of the e3 ubiquitin-2 protein ligase uhrf1 in complex with trimethylated histone h3-k93 peptide
12c1h4uA_



8.7 18 PDB header:extracellular matrix protein
Chain: A: PDB Molecule:nidogen-1;
PDBTitle: domain g2 of mouse nidogen-1
13d1v9la2



8.3 14 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Aminoacid dehydrogenases
14d1hwxa2



8.1 14 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Aminoacid dehydrogenases
15d1bgva2



8.0 16 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Aminoacid dehydrogenases
16c1piqA_



8.0 18 PDB header:dna binding protein
Chain: A: PDB Molecule:protein (general control protein gcn4-piq);
PDBTitle: crystal structure of gcn4-piq, a trimeric coiled coil with buried2 polar residues
17d1jb0j_



7.3 17 Fold:Single transmembrane helix
Superfamily:Subunit IX of photosystem I reaction centre, PsaJ
Family:Subunit IX of photosystem I reaction centre, PsaJ
18c2o01J_



7.3 17 PDB header:photosynthesis
Chain: J: PDB Molecule:photosystem i reaction center subunit ix;
PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution
19d1euza2



7.1 13 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Aminoacid dehydrogenases
20d1xo8a_



6.9 9 Fold:Immunoglobulin-like beta-sandwich
Superfamily:LEA14-like
Family:LEA14-like
21d1bvua2



not modelled 6.7 9 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Aminoacid dehydrogenases
22c1v9lA_



not modelled 6.2 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:glutamate dehydrogenase;
PDBTitle: l-glutamate dehydrogenase from pyrobaculum islandicum2 complexed with nad
23c2e6gI_



not modelled 6.2 32 PDB header:hydrolase
Chain: I: PDB Molecule:5'-nucleotidase sure;
PDBTitle: crystal structure of the stationary phase survival protein sure from2 thermus thermophilus hb8 in complex with phosphate
24d1ikta_



not modelled 6.1 16 Fold:SCP-like
Superfamily:SCP-like
Family:Sterol carrier protein, SCP
25c2wpzA_



not modelled 6.1 16 PDB header:transcription
Chain: A: PDB Molecule:general control protein gcn4;
PDBTitle: gcn4 leucine zipper mutant with two vxxnxxx motifs2 coordinating chloride
26d1g3wa2



not modelled 5.8 17 Fold:Iron-dependent repressor protein, dimerization domain
Superfamily:Iron-dependent repressor protein, dimerization domain
Family:Iron-dependent repressor protein, dimerization domain
27c2wpzB_



not modelled 5.8 16 PDB header:transcription
Chain: B: PDB Molecule:general control protein gcn4;
PDBTitle: gcn4 leucine zipper mutant with two vxxnxxx motifs2 coordinating chloride
28c2wpzC_



not modelled 5.6 16 PDB header:transcription
Chain: C: PDB Molecule:general control protein gcn4;
PDBTitle: gcn4 leucine zipper mutant with two vxxnxxx motifs2 coordinating chloride
29d1l5xa_



not modelled 5.6 12 Fold:SurE-like
Superfamily:SurE-like
Family:SurE-like
30c3aogA_



not modelled 5.6 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:glutamate dehydrogenase;
PDBTitle: crystal structure of glutamate dehydrogenase (gdhb) from thermus2 thermophilus (glu bound form)
31c2ccfA_



not modelled 5.3 24 PDB header:four helix bundle
Chain: A: PDB Molecule:general control protein gcn4;
PDBTitle: antiparallel configuration of pli e20s
32d1gtma2



not modelled 5.3 12 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Aminoacid dehydrogenases
33c1unyB_



not modelled 5.2 24 PDB header:four helix bundle
Chain: B: PDB Molecule:general control protein gcn4;
PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles
34c1gcmA_



not modelled 5.1 18 PDB header:transcription regulation
Chain: A: PDB Molecule:gcn4p-ii;
PDBTitle: gcn4 leucine zipper core mutant p-li
35c1uo0B_



not modelled 5.1 24 PDB header:four helix bundle
Chain: B: PDB Molecule:general control protein gcn4;
PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles
36c1uo0A_



not modelled 5.1 24 PDB header:four helix bundle
Chain: A: PDB Molecule:general control protein gcn4;
PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles
37c1uo1B_



not modelled 5.1 24 PDB header:four helix bundle
Chain: B: PDB Molecule:general control protein gcn4;
PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles
38c1uo1A_



not modelled 5.1 24 PDB header:four helix bundle
Chain: A: PDB Molecule:general control protein gcn4;
PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles
39c1unwB_



not modelled 5.1 24 PDB header:four helix bundle
Chain: B: PDB Molecule:general control protein gcn4;
PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles
40c1gclD_



not modelled 5.0 24 PDB header:leucine zipper
Chain: D: PDB Molecule:gcn4;
PDBTitle: gcn4 leucine zipper core mutant p-li
41c1gclB_



not modelled 5.0 24 PDB header:leucine zipper
Chain: B: PDB Molecule:gcn4;
PDBTitle: gcn4 leucine zipper core mutant p-li
42c1gclC_



not modelled 5.0 24 PDB header:leucine zipper
Chain: C: PDB Molecule:gcn4;
PDBTitle: gcn4 leucine zipper core mutant p-li
43c1gclA_



not modelled 5.0 24 PDB header:leucine zipper
Chain: A: PDB Molecule:gcn4;
PDBTitle: gcn4 leucine zipper core mutant p-li

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