Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP76345
DateThu Jan 5 12:22:07 GMT 2012
Unique Job IDde3bd159abd8154a

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1kqfc_
Top template information
Fold:Heme-binding four-helical bundle
Superfamily:Transmembrane di-heme cytochromes
Family:Formate dehydrogenase N, cytochrome (gamma) subunit
Confidence and coverage
Confidence: 99.9% Coverage: 90%
159 residues ( 90% of your sequence) have been modelled with 99.9% 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  MNRFSKTQIYLHWITLLFVAITYAAMELRGWFPKGSSTYLLMRETHYNAGIFVWVLMFSR
Secondary structure 









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Disorder  ?????






















































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
















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Disorder 






?
????????










































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   .........130.........140.........150.........160.........170......
Sequence  SPFVTPNSEIKALIKNIHETWANIGYFLIAAHAGAALFHHYIQKDNTLLRMMPRRK
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 1kqf chain C

3D model

Region: 1 - 176
Aligned: 159
Modelled: 176
Confidence: 99.9%
Identity: 16%
Fold: Heme-binding four-helical bundle
Superfamily: Transmembrane di-heme cytochromes
Family: Formate dehydrogenase N, cytochrome (gamma) subunit

Phyre2

PDB 2qjk chain M

3D model

Region: 14 - 159
Aligned: 136
Modelled: 146
Confidence: 95.2%
Identity: 13%
PDB header:electron transport
Chain: M: PDB Molecule:cytochrome b;
PDBTitle: crystal structure analysis of mutant rhodobacter2 sphaeroides bc1 with stigmatellin and antimycin

Phyre2

PDB 3cx5 chain N

3D model

Region: 14 - 159
Aligned: 136
Modelled: 146
Confidence: 94.9%
Identity: 15%
PDB header:oxidoreductase
Chain: N: PDB Molecule:cytochrome b;
PDBTitle: structure of complex iii with bound cytochrome c in reduced2 state and definition of a minimal core interface for3 electron transfer.

Phyre2

PDB 3cwb chain C

3D model

Region: 14 - 159
Aligned: 134
Modelled: 146
Confidence: 94.6%
Identity: 15%
PDB header:oxidoreductase
Chain: C: PDB Molecule:cytochrome b;
PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d

Phyre2

PDB 3cx5 chain C domain 2

3D model

Region: 14 - 159
Aligned: 139
Modelled: 139
Confidence: 93.5%
Identity: 15%
Fold: Heme-binding four-helical bundle
Superfamily: Transmembrane di-heme cytochromes
Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Phyre2

PDB 1ppj chain C domain 2

3D model

Region: 14 - 159
Aligned: 134
Modelled: 146
Confidence: 93.2%
Identity: 12%
Fold: Heme-binding four-helical bundle
Superfamily: Transmembrane di-heme cytochromes
Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Phyre2

PDB 2e74 chain A domain 1

3D model

Region: 14 - 159
Aligned: 136
Modelled: 146
Confidence: 91.3%
Identity: 15%
Fold: Heme-binding four-helical bundle
Superfamily: Transmembrane di-heme cytochromes
Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Phyre2

PDB 1bcc chain C domain 3

3D model

Region: 14 - 159
Aligned: 134
Modelled: 146
Confidence: 91.3%
Identity: 14%
Fold: Heme-binding four-helical bundle
Superfamily: Transmembrane di-heme cytochromes
Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Phyre2

PDB 1q90 chain B

3D model

Region: 14 - 159
Aligned: 136
Modelled: 146
Confidence: 91.2%
Identity: 12%
Fold: Heme-binding four-helical bundle
Superfamily: Transmembrane di-heme cytochromes
Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Phyre2

PDB 1y5i chain C domain 1

3D model

Region: 5 - 150
Aligned: 136
Modelled: 146
Confidence: 60.9%
Identity: 9%
Fold: Heme-binding four-helical bundle
Superfamily: Respiratory nitrate reductase 1 gamma chain
Family: Respiratory nitrate reductase 1 gamma chain

Phyre2

PDB 2ftc chain Q

3D model

Region: 167 - 176
Aligned: 10
Modelled: 10
Confidence: 20.2%
Identity: 50%
PDB header:ribosome
Chain: Q: PDB Molecule:39s ribosomal protein l34, mitochondrial;
PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome

Phyre2

PDB 1t33 chain A domain 1

3D model

Region: 155 - 172
Aligned: 18
Modelled: 18
Confidence: 12.9%
Identity: 22%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Tetracyclin repressor-like, N-terminal domain

Phyre2

PDB 2bs2 chain C domain 1

3D model

Region: 117 - 156
Aligned: 40
Modelled: 40
Confidence: 10.4%
Identity: 8%
Fold: Heme-binding four-helical bundle
Superfamily: Fumarate reductase respiratory complex transmembrane subunits
Family: Fumarate reductase respiratory complex cytochrome b subunit, FrdC

Phyre2

PDB 2yvh chain A

3D model

Region: 155 - 172
Aligned: 18
Modelled: 16
Confidence: 9.2%
Identity: 22%
PDB header:transcription/dna
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of the operator-binding form of the multi-drug2 binding transcriptional repressor cgmr

Phyre2

PDB 2rae chain A

3D model

Region: 155 - 172
Aligned: 18
Modelled: 18
Confidence: 8.5%
Identity: 17%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, acrr family protein;
PDBTitle: crystal structure of a tetr/acrr family transcriptional regulator from2 rhodococcus sp. rha1

Phyre2

PDB 2guh chain A

3D model

Region: 155 - 172
Aligned: 18
Modelled: 18
Confidence: 7.6%
Identity: 6%
PDB header:transcription
Chain: A: PDB Molecule:putative tetr-family transcriptional regulator;
PDBTitle: crystal structure of the putative tetr-family transcriptional2 regulator from rhodococcus sp. rha1

Phyre2

PDB 2d6y chain A domain 1

3D model

Region: 155 - 172
Aligned: 18
Modelled: 18
Confidence: 7.3%
Identity: 11%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Tetracyclin repressor-like, N-terminal domain

Phyre2

PDB 2hku chain A domain 1

3D model

Region: 155 - 168
Aligned: 14
Modelled: 14
Confidence: 7.3%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Tetracyclin repressor-like, N-terminal domain

Phyre2

PDB 2id6 chain A domain 1

3D model

Region: 155 - 172
Aligned: 18
Modelled: 18
Confidence: 7.2%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Tetracyclin repressor-like, N-terminal domain

Phyre2

PDB 1z0x chain A

3D model

Region: 155 - 172
Aligned: 18
Modelled: 16
Confidence: 7.1%
Identity: 17%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of transcriptional regulator, tetr family from2 enterococcus faecalis v583

Phyre2
1

d1kqfc_
2

c2qjkM_
3

c3cx5N_
4

c3cwbC_
5

d3cx5c2
6

d1ppjc2
7

d2e74a1
8

d1bccc3
9

d1q90b_
10

d1y5ic1
11

c2ftcQ_
12

d1t33a1
13

d2bs2c1
14

c2yvhA_
15

c2raeA_
16

c2guhA_
17

d2d6ya1
18

d2hkua1
19

d2id6a1
20

c1z0xA_
21



22



23



24



25



26



27



28



29



30



31



32



33



34



35



36



37



38



39



40



41






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1kqfc_



99.9 16 Fold:Heme-binding four-helical bundle
Superfamily:Transmembrane di-heme cytochromes
Family:Formate dehydrogenase N, cytochrome (gamma) subunit
2c2qjkM_



95.2 13 PDB header:electron transport
Chain: M: PDB Molecule:cytochrome b;
PDBTitle: crystal structure analysis of mutant rhodobacter2 sphaeroides bc1 with stigmatellin and antimycin
3c3cx5N_



94.9 15 PDB header:oxidoreductase
Chain: N: PDB Molecule:cytochrome b;
PDBTitle: structure of complex iii with bound cytochrome c in reduced2 state and definition of a minimal core interface for3 electron transfer.
4c3cwbC_



94.6 15 PDB header:oxidoreductase
Chain: C: PDB Molecule:cytochrome b;
PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d
5d3cx5c2



93.5 15 Fold:Heme-binding four-helical bundle
Superfamily:Transmembrane di-heme cytochromes
Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
6d1ppjc2



93.2 12 Fold:Heme-binding four-helical bundle
Superfamily:Transmembrane di-heme cytochromes
Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
7d2e74a1



91.3 15 Fold:Heme-binding four-helical bundle
Superfamily:Transmembrane di-heme cytochromes
Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
8d1bccc3



91.3 14 Fold:Heme-binding four-helical bundle
Superfamily:Transmembrane di-heme cytochromes
Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
9d1q90b_



91.2 12 Fold:Heme-binding four-helical bundle
Superfamily:Transmembrane di-heme cytochromes
Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
10d1y5ic1



60.9 9 Fold:Heme-binding four-helical bundle
Superfamily:Respiratory nitrate reductase 1 gamma chain
Family:Respiratory nitrate reductase 1 gamma chain
11c2ftcQ_



20.2 50 PDB header:ribosome
Chain: Q: PDB Molecule:39s ribosomal protein l34, mitochondrial;
PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome
12d1t33a1



12.9 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
13d2bs2c1



10.4 8 Fold:Heme-binding four-helical bundle
Superfamily:Fumarate reductase respiratory complex transmembrane subunits
Family:Fumarate reductase respiratory complex cytochrome b subunit, FrdC
14c2yvhA_



9.2 22 PDB header:transcription/dna
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of the operator-binding form of the multi-drug2 binding transcriptional repressor cgmr
15c2raeA_



8.5 17 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, acrr family protein;
PDBTitle: crystal structure of a tetr/acrr family transcriptional regulator from2 rhodococcus sp. rha1
16c2guhA_



7.6 6 PDB header:transcription
Chain: A: PDB Molecule:putative tetr-family transcriptional regulator;
PDBTitle: crystal structure of the putative tetr-family transcriptional2 regulator from rhodococcus sp. rha1
17d2d6ya1



7.3 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
18d2hkua1



7.3 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
19d2id6a1



7.2 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
20c1z0xA_



7.1 17 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of transcriptional regulator, tetr family from2 enterococcus faecalis v583
21d1z0xa1



not modelled 6.8 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
22d2gfna1



not modelled 6.7 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
23d2axtc1



not modelled 6.6 8 Fold:Photosystem II antenna protein-like
Superfamily:Photosystem II antenna protein-like
Family:Photosystem II antenna protein-like
24c2axtc_



not modelled 6.6 8 PDB header:electron transport
Chain: C: PDB Molecule:photosystem ii cp43 protein;
PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus
25d2g3ba1



not modelled 6.5 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
26c2dg8D_



not modelled 6.3 11 PDB header:gene regulation
Chain: D: PDB Molecule:putative tetr-family transcriptional regulatory protein;
PDBTitle: crystal structure of the putative trasncriptional regulator sco75182 from streptomyces coelicolor a3(2)
27d2fx0a1



not modelled 6.3 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
28c2fbqA_



not modelled 6.2 22 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional regulator;
PDBTitle: the crystal structure of transcriptional regulator pa3006
29c2wgbB_



not modelled 6.0 14 PDB header:transcription
Chain: B: PDB Molecule:tetr family transcriptional repressor lfrr;
PDBTitle: crystal structure of the tetr-like transcriptional2 regulator lfrr from mycobacterium smegmatis
30d2o7ta1



not modelled 6.0 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
31c2kncA_



not modelled 5.9 2 PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
32d2id3a1



not modelled 5.8 0 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
33d2vkea1



not modelled 5.7 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
34c2ogfD_



not modelled 5.7 40 PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:hypothetical protein mj0408;
PDBTitle: crystal structure of protein mj0408 from methanococcus jannaschii,2 pfam duf372
35d1v7ba1



not modelled 5.6 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
36d2i52a1



not modelled 5.6 40 Fold:MK0786-like
Superfamily:MK0786-like
Family:MK0786-like
37d2axtb1



not modelled 5.6 14 Fold:Photosystem II antenna protein-like
Superfamily:Photosystem II antenna protein-like
Family:Photosystem II antenna protein-like
38c2qibA_



not modelled 5.4 11 PDB header:transcription
Chain: A: PDB Molecule:tetr-family transcriptional regulator;
PDBTitle: crystal structure of tetr-family transcriptional regulator from2 streptomyces coelicolor
39c3fiwB_



not modelled 5.3 17 PDB header:transcription regulator
Chain: B: PDB Molecule:putative tetr-family transcriptional regulator;
PDBTitle: structure of sco0253, a tetr-family transcriptional regulator from2 streptomyces coelicolor
40d1vi0a1



not modelled 5.3 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
41c3cwrA_



not modelled 5.3 6 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of transcriptional regulator of tetr2 family (yp_425770.1) from rhodospirillum rubrum atcc 111703 at 1.50 a resolution

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