Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	R	F	L	E	N	A	M	Y	A	S	R	W	L	L	A	P	V	Y	F	G	L	S	L	A	L	V	A	L	A	L	K	F	F	Q	E	I	I	H	V	L	P	N	I	F	S	M	A	E	S	D	L	I	L	V	L	L	S	L
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	D	M	T	L	V	G	G	L	L	V	M	V	M	F	S	G	Y	E	N	F	V	S	Q	L	D	I	S	E	N	K	E	K	L	N	W	L	G	K	M	D	A	T	S	L	K	N	K	V	A	A	S	I	V	A	I	S	S	I	H
Secondary structure
SS confidence
Disorder																										?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.
Sequence		L	L	R	V	F	M	D	A	K	N	V	P	D	N	K	L	M	W	Y	V	I	I	H	L	T	F	V	L	S	A	F	V	M	G	Y	L	D	R	L	T	R	H	N	H
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 1q90 chain B Region: 110 - 153 Aligned: 44 Modelled: 44 Confidence: 36.6% 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 2e74 chain A domain 1 Region: 110 - 153 Aligned: 44 Modelled: 44 Confidence: 31.9% Identity: 20% 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 C domain 2 Region: 110 - 153 Aligned: 44 Modelled: 44 Confidence: 24.2% Identity: 11% 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: 110 - 153 Aligned: 44 Modelled: 44 Confidence: 16.8% Identity: 11% 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 2qjk chain M Region: 110 - 153 Aligned: 44 Modelled: 44 Confidence: 16.0% Identity: 14% 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 2au5 chain A domain 1 Region: 59 - 98 Aligned: 38 Modelled: 40 Confidence: 12.2% Identity: 18% Fold: EF2947-like Superfamily: EF2947-like Family: EF2947-like Phyre2 PDB 1p4q chain A Region: 85 - 103 Aligned: 19 Modelled: 19 Confidence: 11.0% Identity: 26% PDB header:transcription/transferase Chain: A: PDB Molecule:cbp/p300-interacting transactivator 2; PDBTitle: solution structure of the cited2 transactivation domain in2 complex with the p300 ch1 domain Phyre2 PDB 2vkj chain A Region: 72 - 115 Aligned: 37 Modelled: 44 Confidence: 10.1% Identity: 43% PDB header:membrane protein Chain: A: PDB Molecule:tm1634; PDBTitle: structure of the soluble domain of the membrane protein2 tm1634 from thermotoga maritima Phyre2 PDB 2yv4 chain A Region: 150 - 164 Aligned: 14 Modelled: 15 Confidence: 9.0% Identity: 14% PDB header:rna binding protein Chain: A: PDB Molecule:hypothetical protein ph0435; PDBTitle: crystal structure of c-terminal sua5 domain from pyrococcus horikoshii2 hypothetical sua5 protein ph0435 Phyre2 PDB 2p62 chain A domain 1 Region: 76 - 84 Aligned: 9 Modelled: 9 Confidence: 8.3% Identity: 22% Fold: PH0156-like Superfamily: PH0156-like Family: PH0156-like Phyre2 PDB 2hkj chain A domain 1 Region: 93 - 143 Aligned: 50 Modelled: 51 Confidence: 8.3% Identity: 14% Fold: S13-like H2TH domain Superfamily: S13-like H2TH domain Family: Topoisomerase VI-B subunit middle domain Phyre2 PDB 1r8u chain A Region: 85 - 103 Aligned: 19 Modelled: 19 Confidence: 8.1% Identity: 26% PDB header:transcription/transcription activator Chain: A: PDB Molecule:cbp/p300-interacting transactivator 2; PDBTitle: nmr structure of cbp taz1/cited2 complex Phyre2 PDB 1ppj chain C domain 2 Region: 110 - 153 Aligned: 42 Modelled: 44 Confidence: 7.6% 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 2e9x chain B domain 1 Region: 94 - 108 Aligned: 15 Modelled: 15 Confidence: 7.3% Identity: 7% Fold: GINS helical bundle-like Superfamily: GINS helical bundle-like Family: PSF2 C-terminal domain-like Phyre2 PDB 2wp0 chain C Region: 78 - 124 Aligned: 47 Modelled: 47 Confidence: 7.3% Identity: 19% PDB header:dna binding protein Chain: C: PDB Molecule:chromosomal replication initiator protein dnaa; PDBTitle: crystal structure of a hoba-dnaa (domain i-ii) complex from2 helicobacter pylori. Phyre2 1 d1q90b_ 2 d2e74a1 3 d3cx5c2 4 c3cx5N_ 5 c2qjkM_ 6 d2au5a1 7 c1p4qA_ 8 c2vkjA_ 9 c2yv4A_ 10 d2p62a1 11 d2hkja1 12 c1r8uA_ 13 d1ppjc2 14 d2e9xb1 15 c2wp0C_

Detailed template information

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

1 d1q90b_ 36.6 18 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 2 d2e74a1 31.9 20 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 3 d3cx5c2 24.2 11 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 4 c3cx5N_ 16.8 11 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 c2qjkM_ 16.0 14 PDB header:electron transport Chain: M: PDB Molecule:cytochrome b; PDBTitle: crystal structure analysis of mutant rhodobacter2 sphaeroides bc1 with stigmatellin and antimycin 6 d2au5a1 12.2 18 Fold:EF2947-like Superfamily:EF2947-like Family:EF2947-like 7 c1p4qA_ 11.0 26 PDB header:transcription/transferase Chain: A: PDB Molecule:cbp/p300-interacting transactivator 2; PDBTitle: solution structure of the cited2 transactivation domain in2 complex with the p300 ch1 domain 8 c2vkjA_ 10.1 43 PDB header:membrane protein Chain: A: PDB Molecule:tm1634; PDBTitle: structure of the soluble domain of the membrane protein2 tm1634 from thermotoga maritima 9 c2yv4A_ 9.0 14 PDB header:rna binding protein Chain: A: PDB Molecule:hypothetical protein ph0435; PDBTitle: crystal structure of c-terminal sua5 domain from pyrococcus horikoshii2 hypothetical sua5 protein ph0435 10 d2p62a1 8.3 22 Fold:PH0156-like Superfamily:PH0156-like Family:PH0156-like 11 d2hkja1 8.3 14 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Topoisomerase VI-B subunit middle domain 12 c1r8uA_ 8.1 26 PDB header:transcription/transcription activator Chain: A: PDB Molecule:cbp/p300-interacting transactivator 2; PDBTitle: nmr structure of cbp taz1/cited2 complex 13 d1ppjc2 7.6 14 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 14 d2e9xb1 7.3 7 Fold:GINS helical bundle-like Superfamily:GINS helical bundle-like Family:PSF2 C-terminal domain-like 15 c2wp0C_ 7.3 19 PDB header:dna binding protein Chain: C: PDB Molecule:chromosomal replication initiator protein dnaa; PDBTitle: crystal structure of a hoba-dnaa (domain i-ii) complex from2 helicobacter pylori.

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