Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	F	T	N	T	P	E	R	Y	G	V	I	S	A	A	F	H	W	L	S	A	I	I	V	Y	G	M	F	A	L	G	L	W	M	V	T	L	S	Y	Y	D	G	W	Y	H	K	A	P	E	L	H	K	S	I	G	I	L	L	M
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	G	L	V	I	R	V	L	W	R	V	I	S	P	P	P	G	P	L	P	S	Y	S	P	M	T	R	L	A	A	R	A	G	H	L	A	L	Y	L	L	L	F	A	I	G	I	S	G	Y	L	I	S	T	A	D	G	K	P	I	S
Secondary structure
SS confidence
Disorder																	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	F	G	W	F	D	V	P	A	T	L	A	D	A	G	A	Q	A	D	F	A	G	A	L	H	F	W	L	A	W	S	V	V	V	L	S	V	M	H	G	F	M	A	L	K	H	H	F	I	D	K	D	D	T	L	K	R	M	L	G
Secondary structure
SS confidence
Disorder										?			?
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		K	S	S	S	D	Y	G	V
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

Rank Aligned region

PDB 1kqf chain C Region: 2 - 182 Aligned: 163 Modelled: 168 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 Region: 20 - 166 Aligned: 140 Modelled: 147 Confidence: 97.1% 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 C domain 2 Region: 20 - 185 Aligned: 153 Modelled: 166 Confidence: 97.0% 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 3cx5 chain N Region: 20 - 185 Aligned: 153 Modelled: 166 Confidence: 97.0% Identity: 14% 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 1q90 chain B Region: 20 - 174 Aligned: 142 Modelled: 155 Confidence: 96.9% Identity: 18% 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 Region: 20 - 185 Aligned: 151 Modelled: 166 Confidence: 96.5% Identity: 16% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 3cwb chain C Region: 20 - 185 Aligned: 151 Modelled: 166 Confidence: 96.5% Identity: 16% 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 1bcc chain C domain 3 Region: 20 - 185 Aligned: 151 Modelled: 166 Confidence: 96.5% Identity: 17% 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 Region: 20 - 174 Aligned: 142 Modelled: 155 Confidence: 96.4% Identity: 18% 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 Region: 1 - 157 Aligned: 147 Modelled: 157 Confidence: 67.7% Identity: 14% Fold: Heme-binding four-helical bundle Superfamily: Respiratory nitrate reductase 1 gamma chain Family: Respiratory nitrate reductase 1 gamma chain Phyre2 PDB 2iec chain A domain 1 Region: 161 - 170 Aligned: 10 Modelled: 10 Confidence: 20.4% Identity: 30% Fold: MK0786-like Superfamily: MK0786-like Family: MK0786-like Phyre2 PDB 2ogf chain D Region: 161 - 170 Aligned: 10 Modelled: 10 Confidence: 17.5% Identity: 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 Phyre2 PDB 2i52 chain A domain 1 Region: 161 - 170 Aligned: 10 Modelled: 10 Confidence: 16.9% Identity: 20% Fold: MK0786-like Superfamily: MK0786-like Family: MK0786-like Phyre2 PDB 1t33 chain A domain 1 Region: 162 - 179 Aligned: 18 Modelled: 18 Confidence: 10.4% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Tetracyclin repressor-like, N-terminal domain Phyre2 PDB 3g56 chain A Region: 162 - 179 Aligned: 18 Modelled: 18 Confidence: 7.6% Identity: 39% PDB header:dna binding protein Chain: A: PDB Molecule:regulator of macrolide 2'-phosphotransferase i; PDBTitle: structure of the macrolide biosensor protein, mphr(a) Phyre2 PDB 1m56 chain D Region: 1 - 34 Aligned: 34 Modelled: 34 Confidence: 7.4% Identity: 21% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 PDB 2yvh chain A Region: 162 - 179 Aligned: 18 Modelled: 16 Confidence: 7.2% 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 2hku chain B Region: 162 - 175 Aligned: 14 Modelled: 14 Confidence: 6.9% Identity: 7% PDB header:transcription regulator Chain: B: PDB Molecule:a putative transcriptional regulator; PDBTitle: structural genomics, the crystal structure of a putative2 transcriptional regulator from rhodococcus sp. rha1 Phyre2 PDB 3nnr chain A Region: 162 - 179 Aligned: 18 Modelled: 18 Confidence: 6.8% Identity: 28% PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, tetr family; PDBTitle: crystal structure of a tetr-family transcriptional regulator2 (maqu_3571) from marinobacter aquaeolei vt8 at 2.49 a resolution Phyre2 PDB 2guh chain A Region: 162 - 179 Aligned: 18 Modelled: 18 Confidence: 6.6% Identity: 11% 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 1 d1kqfc_ 2 c2qjkM_ 3 d3cx5c2 4 c3cx5N_ 5 d1q90b_ 6 d1ppjc2 7 c3cwbC_ 8 d1bccc3 9 d2e74a1 10 d1y5ic1 11 d2ieca1 12 c2ogfD_ 13 d2i52a1 14 d1t33a1 15 c3g56A_ 16 d1m56d_ 17 c2yvhA_ 18 c2hkuB_ 19 c3nnrA_ 20 c2guhA_ 21 22 23 24 25 26 27 28 29 30 31

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 d1kqfc_ 99.9 16 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Formate dehydrogenase N, cytochrome (gamma) subunit 2 c2qjkM_ 97.1 13 PDB header:electron transport Chain: M: PDB Molecule:cytochrome b; PDBTitle: crystal structure analysis of mutant rhodobacter2 sphaeroides bc1 with stigmatellin and antimycin 3 d3cx5c2 97.0 12 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 4 c3cx5N_ 97.0 14 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. 5 d1q90b_ 96.9 18 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 6 d1ppjc2 96.5 16 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 7 c3cwbC_ 96.5 16 PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome b; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d 8 d1bccc3 96.5 17 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 9 d2e74a1 96.4 18 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 10 d1y5ic1 67.7 14 Fold:Heme-binding four-helical bundle Superfamily:Respiratory nitrate reductase 1 gamma chain Family:Respiratory nitrate reductase 1 gamma chain 11 d2ieca1 20.4 30 Fold:MK0786-like Superfamily:MK0786-like Family:MK0786-like 12 c2ogfD_ 17.5 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 13 d2i52a1 16.9 20 Fold:MK0786-like Superfamily:MK0786-like Family:MK0786-like 14 d1t33a1 10.4 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 15 c3g56A_ 7.6 39 PDB header:dna binding protein Chain: A: PDB Molecule:regulator of macrolide 2'-phosphotransferase i; PDBTitle: structure of the macrolide biosensor protein, mphr(a) 16 d1m56d_ 7.4 21 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 17 c2yvhA_ 7.2 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 18 c2hkuB_ 6.9 7 PDB header:transcription regulator Chain: B: PDB Molecule:a putative transcriptional regulator; PDBTitle: structural genomics, the crystal structure of a putative2 transcriptional regulator from rhodococcus sp. rha1 19 c3nnrA_ 6.8 28 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, tetr family; PDBTitle: crystal structure of a tetr-family transcriptional regulator2 (maqu_3571) from marinobacter aquaeolei vt8 at 2.49 a resolution 20 c2guhA_ 6.6 11 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 21 c1z0xA_ not modelled 6.5 22 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, tetr family; PDBTitle: crystal structure of transcriptional regulator, tetr family from2 enterococcus faecalis v583 22 d2hkua1 not modelled 6.3 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 23 d2d6ya1 not modelled 6.0 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 24 c2wgbB_ not modelled 5.8 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 25 d2id6a1 not modelled 5.7 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 26 c2raeA_ not modelled 5.6 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 27 d1z0xa1 not modelled 5.3 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 28 c2dg8D_ not modelled 5.2 17 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) 29 d2gfna1 not modelled 5.2 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 30 d2g3ba1 not modelled 5.1 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 31 d2o7ta1 not modelled 5.1 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain

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

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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