Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	Q	S	V	L	L	P	P	G	P	F	T	R	R	Q	A	Q	A	V	T	T	T	Y	S	N	I	T	L	E	D	D	Q	G	S	H	F	R	L	V	V	R	D	T	E	G	R	M	V	W	R	A	W	N	F	E	P	D	A	G
Secondary structure
SS confidence
Disorder		?	?	?	?			?	?		?	?	?	?																																													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.
Sequence		E	G	L	N	R	Y	I	R	T	S	G	I	R	T	D	T	A	T	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 domain 1 Region: 10 - 75 Aligned: 66 Modelled: 66 Confidence: 100.0% Identity: 100% Fold: dsRBD-like Superfamily: YcfA/nrd intein domain Family: YkfF-like Phyre2 PDB 2hjj chain A Region: 10 - 75 Aligned: 66 Modelled: 66 Confidence: 100.0% Identity: 100% 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 3fcg chain B Region: 4 - 47 Aligned: 27 Modelled: 29 Confidence: 26.9% Identity: 26% PDB header:membrane protein, protein transport Chain: B: PDB Molecule:f1 capsule-anchoring protein; PDBTitle: crystal structure analysis of the middle domain of the2 caf1a usher Phyre2 PDB 3isy chain A Region: 27 - 51 Aligned: 25 Modelled: 25 Confidence: 22.9% Identity: 36% 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: 34 - 57 Aligned: 24 Modelled: 24 Confidence: 19.2% Identity: 29% 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 3ffe chain B Region: 25 - 50 Aligned: 26 Modelled: 26 Confidence: 17.2% Identity: 31% PDB header:biosynthetic protein Chain: B: PDB Molecule:acsd; PDBTitle: structure of achromobactin synthetase protein d, (acsd) Phyre2 PDB 1xs3 chain A Region: 27 - 41 Aligned: 15 Modelled: 15 Confidence: 16.3% Identity: 27% 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: 15 - 41 Aligned: 27 Modelled: 27 Confidence: 16.1% Identity: 19% PDB header:protein binding Chain: A: PDB Molecule:protein bola; PDBTitle: solution structure of the bola protein from escherichia coli Phyre2 PDB 1xdn chain A Region: 27 - 49 Aligned: 23 Modelled: 23 Confidence: 14.7% Identity: 17% Fold: ATP-grasp Superfamily: DNA ligase/mRNA capping enzyme, catalytic domain Family: RNA ligase Phyre2 PDB 1k1s chain A domain 1 Region: 2 - 40 Aligned: 38 Modelled: 39 Confidence: 13.8% Identity: 16% Fold: Lesion bypass DNA polymerase (Y-family), little finger domain Superfamily: Lesion bypass DNA polymerase (Y-family), little finger domain Family: Lesion bypass DNA polymerase (Y-family), little finger domain Phyre2 PDB 2w02 chain A Region: 25 - 50 Aligned: 26 Modelled: 26 Confidence: 13.0% Identity: 31% PDB header:metal transport Chain: A: PDB Molecule:acsd; PDBTitle: co-complex structure of achromobactin synthetase protein d (2 acsd) with atp from pectobacterium chrysanthemi Phyre2 PDB 3tr3 chain A Region: 27 - 41 Aligned: 15 Modelled: 15 Confidence: 11.7% Identity: 33% 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: 60 - 71 Aligned: 12 Modelled: 12 Confidence: 11.1% 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 2flz chain C Region: 5 - 51 Aligned: 47 Modelled: 47 Confidence: 10.6% Identity: 13% PDB header:hydrolase Chain: C: PDB Molecule:cis-3-chloroacrylic acid dehalogenase; PDBTitle: the x-ray structure of cis-3-chloroacrylic acid dehalogenase (cis-2 caad) with a sulfate ion bound in the active site Phyre2 PDB 3o2e chain A Region: 27 - 41 Aligned: 15 Modelled: 15 Confidence: 10.3% Identity: 20% PDB header:unknown function Chain: A: PDB Molecule:bola-like protein; PDBTitle: crystal structure of a bol-like protein from babesia bovis Phyre2 PDB 2zt9 chain F Region: 59 - 72 Aligned: 14 Modelled: 14 Confidence: 9.5% Identity: 36% 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 2kdn chain A Region: 27 - 41 Aligned: 15 Modelled: 15 Confidence: 9.4% Identity: 33% 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 3lrm chain B Region: 21 - 73 Aligned: 47 Modelled: 53 Confidence: 9.2% Identity: 23% PDB header:hydrolase Chain: B: PDB Molecule:alpha-galactosidase 1; PDBTitle: structure of alfa-galactosidase from saccharomyces cerevisiae with2 raffinose Phyre2 PDB 3chx chain F Region: 60 - 71 Aligned: 12 Modelled: 12 Confidence: 8.5% Identity: 50% PDB header:membrane protein Chain: F: PDB Molecule:pmoa; PDBTitle: crystal structure of methylosinus trichosporium ob3b2 particulate methane monooxygenase (pmmo) Phyre2 PDB 1f1s chain A domain 4 Region: 38 - 71 Aligned: 34 Modelled: 34 Confidence: 8.0% Identity: 21% Fold: Supersandwich Superfamily: Galactose mutarotase-like Family: Hyaluronate lyase-like, central domain Phyre2 1 d2hjja1 2 c2hjjA_ 3 c3fcgB_ 4 c3isyA_ 5 c3hx8A_ 6 c3ffeB_ 7 c1xs3A_ 8 c2dhmA_ 9 d1xdna_ 10 d1k1sa1 11 c2w02A_ 12 c3tr3A_ 13 c1yewF_ 14 c2flzC_ 15 c3o2eA_ 16 c2zt9F_ 17 c2kdnA_ 18 c3lrmB_ 19 c3chxF_ 20 d1f1sa4 21 22 23 24 25 26 27 28 29 30 31 32 33

Detailed template information

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

1 d2hjja1 100.0 100 Fold:dsRBD-like Superfamily:YcfA/nrd intein domain Family:YkfF-like 2 c2hjjA_ 100.0 100 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. 3 c3fcgB_ 26.9 26 PDB header:membrane protein, protein transport Chain: B: PDB Molecule:f1 capsule-anchoring protein; PDBTitle: crystal structure analysis of the middle domain of the2 caf1a usher 4 c3isyA_ 22.9 36 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_ 19.2 29 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 c3ffeB_ 17.2 31 PDB header:biosynthetic protein Chain: B: PDB Molecule:acsd; PDBTitle: structure of achromobactin synthetase protein d, (acsd) 7 c1xs3A_ 16.3 27 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein xc975; PDBTitle: solution structure analysis of the xc975 protein 8 c2dhmA_ 16.1 19 PDB header:protein binding Chain: A: PDB Molecule:protein bola; PDBTitle: solution structure of the bola protein from escherichia coli 9 d1xdna_ 14.7 17 Fold:ATP-grasp Superfamily:DNA ligase/mRNA capping enzyme, catalytic domain Family:RNA ligase 10 d1k1sa1 13.8 16 Fold:Lesion bypass DNA polymerase (Y-family), little finger domain Superfamily:Lesion bypass DNA polymerase (Y-family), little finger domain Family:Lesion bypass DNA polymerase (Y-family), little finger domain 11 c2w02A_ 13.0 31 PDB header:metal transport Chain: A: PDB Molecule:acsd; PDBTitle: co-complex structure of achromobactin synthetase protein d (2 acsd) with atp from pectobacterium chrysanthemi 12 c3tr3A_ 11.7 33 PDB header:unknown function Chain: A: PDB Molecule:bola; PDBTitle: structure of a bola protein homologue from coxiella burnetii 13 c1yewF_ 11.1 50 PDB header:oxidoreductase, membrane protein Chain: F: PDB Molecule:particulate methane monooxygenase, a subunit; PDBTitle: crystal structure of particulate methane monooxygenase 14 c2flzC_ 10.6 13 PDB header:hydrolase Chain: C: PDB Molecule:cis-3-chloroacrylic acid dehalogenase; PDBTitle: the x-ray structure of cis-3-chloroacrylic acid dehalogenase (cis-2 caad) with a sulfate ion bound in the active site 15 c3o2eA_ 10.3 20 PDB header:unknown function Chain: A: PDB Molecule:bola-like protein; PDBTitle: crystal structure of a bol-like protein from babesia bovis 16 c2zt9F_ 9.5 36 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 17 c2kdnA_ 9.4 33 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. 18 c3lrmB_ 9.2 23 PDB header:hydrolase Chain: B: PDB Molecule:alpha-galactosidase 1; PDBTitle: structure of alfa-galactosidase from saccharomyces cerevisiae with2 raffinose 19 c3chxF_ 8.5 50 PDB header:membrane protein Chain: F: PDB Molecule:pmoa; PDBTitle: crystal structure of methylosinus trichosporium ob3b2 particulate methane monooxygenase (pmmo) 20 d1f1sa4 8.0 21 Fold:Supersandwich Superfamily:Galactose mutarotase-like Family:Hyaluronate lyase-like, central domain 21 c2f4qA_ not modelled 7.9 26 PDB header:isomerase Chain: A: PDB Molecule:type i topoisomerase, putative; PDBTitle: crystal structure of deinococcus radiodurans topoisomerase ib 22 d1ny8a_ not modelled 7.8 36 Fold:Alpha-lytic protease prodomain-like Superfamily:BolA-like Family:BolA-like 23 c2h7fX_ not modelled 6.5 14 PDB header:isomerase/dna Chain: X: PDB Molecule:dna topoisomerase 1; PDBTitle: structure of variola topoisomerase covalently bound to dna 24 c2knrA_ not modelled 6.5 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atc0905; PDBTitle: solution structure of protein atu0922 from a. tumefaciens. northeast2 structural genomics consortium target att13. ontario center for3 structural proteomics target atc0905 25 d2oa4a1 not modelled 6.3 58 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:SPO1678-like 26 d1v9ja_ not modelled 6.2 33 Fold:Alpha-lytic protease prodomain-like Superfamily:BolA-like Family:BolA-like 27 c3iydB_ not modelled 6.2 19 PDB header:transcription/dna Chain: B: PDB Molecule:dna-directed rna polymerase subunit alpha; PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex 28 d1x7fa2 not modelled 5.8 28 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Outer surface protein, N-terminal domain 29 d1szwa_ not modelled 5.6 30 Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:tRNA pseudouridine synthase TruD 30 c1v60A_ not modelled 5.6 22 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:riken cdna 1810037g04; PDBTitle: solution structure of bola1 protein from mus musculus 31 d1ik0a_ not modelled 5.3 57 Fold:4-helical cytokines Superfamily:4-helical cytokines Family:Short-chain cytokines 32 c2kz3A_ not modelled 5.3 28 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 33 c2k17A_ not modelled 5.3 26 PDB header:transcription Chain: A: PDB Molecule:transcription initiation factor tfiid subunit 3; PDBTitle: solution structure of the taf3 phd domain in complex with a2 h3k4me3 peptide

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