Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	N	S	E	G	W	X	S	F	X	Q	T	L	S	G	L	P	Q	W	A	S	A	D	C	V	A	G	P	L	V	S	A	G	I	T	D	I	N	I	E	D	D	Q	G	I	H	V	R	L	I	V	R	D	A	E	G	R	M	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90
Sequence		W	R	A	W	N	F	E	P	D	A	G	E	G	F	N	R	Y	I	H	R	S	G	I	R	T	D	T	F	P	R
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 2hjj chain A Region: 21 - 86 Aligned: 66 Modelled: 66 Confidence: 100.0% Identity: 62% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ykff; PDBTitle: solution nmr structure of protein ykff from escherichia coli.2 northeast structural genomics target er397. Phyre2 PDB 2hjj chain A domain 1 Region: 21 - 86 Aligned: 66 Modelled: 66 Confidence: 100.0% Identity: 62% Fold: dsRBD-like Superfamily: YcfA/nrd intein domain Family: YkfF-like Phyre2 PDB 3lrm chain B Region: 6 - 84 Aligned: 72 Modelled: 72 Confidence: 39.0% Identity: 18% PDB header:hydrolase Chain: B: PDB Molecule:alpha-galactosidase 1; PDBTitle: structure of alfa-galactosidase from saccharomyces cerevisiae with2 raffinose Phyre2 PDB 3isy chain A Region: 45 - 62 Aligned: 18 Modelled: 18 Confidence: 32.9% Identity: 33% PDB header:protein binding Chain: A: PDB Molecule:intracellular proteinase inhibitor; PDBTitle: crystal structure of an intracellular proteinase inhibitor (ipi,2 bsu11130) from bacillus subtilis at 2.61 a resolution Phyre2 PDB 3hx8 chain A Region: 45 - 68 Aligned: 24 Modelled: 24 Confidence: 12.5% Identity: 25% PDB header:isomerase Chain: A: PDB Molecule:putative ketosteroid isomerase; PDBTitle: crystal structure of putative ketosteroid isomerase2 (np_103587.1) from mesorhizobium loti at 1.45 a resolution Phyre2 PDB 1u2c chain A domain 1 Region: 15 - 57 Aligned: 38 Modelled: 43 Confidence: 12.3% Identity: 18% Fold: Immunoglobulin-like beta-sandwich Superfamily: Cadherin-like Family: Dystroglycan, N-terminal domain Phyre2 PDB 1uas chain A domain 2 Region: 6 - 84 Aligned: 73 Modelled: 73 Confidence: 11.6% Identity: 27% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Amylase, catalytic domain Phyre2 PDB 1xdn chain A Region: 38 - 60 Aligned: 23 Modelled: 23 Confidence: 11.5% Identity: 13% Fold: ATP-grasp Superfamily: DNA ligase/mRNA capping enzyme, catalytic domain Family: RNA ligase Phyre2 PDB 1xs3 chain A Region: 38 - 52 Aligned: 15 Modelled: 15 Confidence: 10.9% Identity: 20% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein xc975; PDBTitle: solution structure analysis of the xc975 protein Phyre2 PDB 2dhm chain A Region: 36 - 52 Aligned: 17 Modelled: 17 Confidence: 9.9% Identity: 12% PDB header:protein binding Chain: A: PDB Molecule:protein bola; PDBTitle: solution structure of the bola protein from escherichia coli Phyre2 PDB 3p1v chain B Region: 19 - 74 Aligned: 56 Modelled: 56 Confidence: 9.2% Identity: 18% PDB header:hydrolase Chain: B: PDB Molecule:metallo-endopeptidase; PDBTitle: crystal structure of a metallo-endopeptidases (bacova_00663) from2 bacteroides ovatus at 1.93 a resolution Phyre2 PDB 1z64 chain A Region: 6 - 12 Aligned: 7 Modelled: 7 Confidence: 8.5% Identity: 57% PDB header:antimicrobial protein Chain: A: PDB Molecule:pleruocidin; PDBTitle: nmr solution structure of pleurocidin in dpc micelles Phyre2 PDB 2zt9 chain F Region: 70 - 83 Aligned: 14 Modelled: 14 Confidence: 8.0% Identity: 29% PDB header:photosynthesis Chain: F: PDB Molecule:cytochrome b6-f complex subunit 7; PDBTitle: crystal structure of the cytochrome b6f complex from nostoc sp. pcc2 7120 Phyre2 PDB 3tr3 chain A Region: 38 - 52 Aligned: 15 Modelled: 15 Confidence: 7.6% Identity: 20% PDB header:unknown function Chain: A: PDB Molecule:bola; PDBTitle: structure of a bola protein homologue from coxiella burnetii Phyre2 PDB 1yew chain F Region: 71 - 82 Aligned: 12 Modelled: 12 Confidence: 7.5% Identity: 50% PDB header:oxidoreductase, membrane protein Chain: F: PDB Molecule:particulate methane monooxygenase, a subunit; PDBTitle: crystal structure of particulate methane monooxygenase Phyre2 PDB 3a23 chain A Region: 26 - 84 Aligned: 54 Modelled: 55 Confidence: 7.4% Identity: 31% PDB header:hydrolase Chain: A: PDB Molecule:putative secreted alpha-galactosidase; PDBTitle: crystal structure of beta-l-arabinopyranosidase complexed with d-2 galactose Phyre2 PDB 3ocj chain A Region: 22 - 52 Aligned: 31 Modelled: 31 Confidence: 7.3% Identity: 26% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative exported protein; PDBTitle: the crystal structure of a possilbe exported protein from bordetella2 parapertussis Phyre2 PDB 2kdn chain A Region: 38 - 52 Aligned: 15 Modelled: 15 Confidence: 7.1% Identity: 13% PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein pfe0790c; PDBTitle: solution structure of pfe0790c, a putative bola-like2 protein from the protozoan parasite plasmodium falciparum. Phyre2 PDB 3o2e chain A Region: 38 - 52 Aligned: 15 Modelled: 15 Confidence: 6.7% Identity: 13% PDB header:unknown function Chain: A: PDB Molecule:bola-like protein; PDBTitle: crystal structure of a bol-like protein from babesia bovis Phyre2 PDB 1x7f chain A domain 2 Region: 60 - 88 Aligned: 29 Modelled: 29 Confidence: 6.5% Identity: 31% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Outer surface protein, N-terminal domain Phyre2 1 c2hjjA_ 2 d2hjja1 3 c3lrmB_ 4 c3isyA_ 5 c3hx8A_ 6 d1u2ca1 7 d1uasa2 8 d1xdna_ 9 c1xs3A_ 10 c2dhmA_ 11 c3p1vB_ 12 c1z64A_ 13 c2zt9F_ 14 c3tr3A_ 15 c1yewF_ 16 c3a23A_ 17 c3ocjA_ 18 c2kdnA_ 19 c3o2eA_ 20 d1x7fa2 21 22 23 24 25

Detailed template information

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

1 c2hjjA_ 100.0 62 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ykff; PDBTitle: solution nmr structure of protein ykff from escherichia coli.2 northeast structural genomics target er397. 2 d2hjja1 100.0 62 Fold:dsRBD-like Superfamily:YcfA/nrd intein domain Family:YkfF-like 3 c3lrmB_ 39.0 18 PDB header:hydrolase Chain: B: PDB Molecule:alpha-galactosidase 1; PDBTitle: structure of alfa-galactosidase from saccharomyces cerevisiae with2 raffinose 4 c3isyA_ 32.9 33 PDB header:protein binding Chain: A: PDB Molecule:intracellular proteinase inhibitor; PDBTitle: crystal structure of an intracellular proteinase inhibitor (ipi,2 bsu11130) from bacillus subtilis at 2.61 a resolution 5 c3hx8A_ 12.5 25 PDB header:isomerase Chain: A: PDB Molecule:putative ketosteroid isomerase; PDBTitle: crystal structure of putative ketosteroid isomerase2 (np_103587.1) from mesorhizobium loti at 1.45 a resolution 6 d1u2ca1 12.3 18 Fold:Immunoglobulin-like beta-sandwich Superfamily:Cadherin-like Family:Dystroglycan, N-terminal domain 7 d1uasa2 11.6 27 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 8 d1xdna_ 11.5 13 Fold:ATP-grasp Superfamily:DNA ligase/mRNA capping enzyme, catalytic domain Family:RNA ligase 9 c1xs3A_ 10.9 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein xc975; PDBTitle: solution structure analysis of the xc975 protein 10 c2dhmA_ 9.9 12 PDB header:protein binding Chain: A: PDB Molecule:protein bola; PDBTitle: solution structure of the bola protein from escherichia coli 11 c3p1vB_ 9.2 18 PDB header:hydrolase Chain: B: PDB Molecule:metallo-endopeptidase; PDBTitle: crystal structure of a metallo-endopeptidases (bacova_00663) from2 bacteroides ovatus at 1.93 a resolution 12 c1z64A_ 8.5 57 PDB header:antimicrobial protein Chain: A: PDB Molecule:pleruocidin; PDBTitle: nmr solution structure of pleurocidin in dpc micelles 13 c2zt9F_ 8.0 29 PDB header:photosynthesis Chain: F: PDB Molecule:cytochrome b6-f complex subunit 7; PDBTitle: crystal structure of the cytochrome b6f complex from nostoc sp. pcc2 7120 14 c3tr3A_ 7.6 20 PDB header:unknown function Chain: A: PDB Molecule:bola; PDBTitle: structure of a bola protein homologue from coxiella burnetii 15 c1yewF_ 7.5 50 PDB header:oxidoreductase, membrane protein Chain: F: PDB Molecule:particulate methane monooxygenase, a subunit; PDBTitle: crystal structure of particulate methane monooxygenase 16 c3a23A_ 7.4 31 PDB header:hydrolase Chain: A: PDB Molecule:putative secreted alpha-galactosidase; PDBTitle: crystal structure of beta-l-arabinopyranosidase complexed with d-2 galactose 17 c3ocjA_ 7.3 26 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative exported protein; PDBTitle: the crystal structure of a possilbe exported protein from bordetella2 parapertussis 18 c2kdnA_ 7.1 13 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein pfe0790c; PDBTitle: solution structure of pfe0790c, a putative bola-like2 protein from the protozoan parasite plasmodium falciparum. 19 c3o2eA_ 6.7 13 PDB header:unknown function Chain: A: PDB Molecule:bola-like protein; PDBTitle: crystal structure of a bol-like protein from babesia bovis 20 d1x7fa2 6.5 31 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Outer surface protein, N-terminal domain 21 c3ffeB_ not modelled 6.2 23 PDB header:biosynthetic protein Chain: B: PDB Molecule:acsd; PDBTitle: structure of achromobactin synthetase protein d, (acsd) 22 c2kz3A_ not modelled 6.1 22 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein rad51l3; PDBTitle: backbone 1h, 13c, and 15n chemical shift assignments for human rad51d2 from 1 to 83 23 d1szna2 not modelled 5.6 27 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 24 c3gv2E_ not modelled 5.6 35 PDB header:viral protein Chain: E: PDB Molecule:fusion protein consisting of capsid protein p24, PDBTitle: x-ray structure of hexameric hiv-1 ca 25 c3chxF_ not modelled 5.3 46 PDB header:membrane protein Chain: F: PDB Molecule:pmoa; PDBTitle: crystal structure of methylosinus trichosporium ob3b2 particulate methane monooxygenase (pmmo)

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