Secondary structure and disorder prediction

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Sequence		M	K	R	L	I	P	V	A	L	L	T	A	L	L	A	G	C	A	H	D	S	P	C	V	P	V	Y	D	D	Q	G	R	L	V	H	T	N	T	C	M	K	G	T	T	Q	D	N	W	E	T	A	G	A	I	A	G	G	A	A	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?									?																									?	?			?	?	?				?					?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.
Sequence		V	A	G	L	T	M	G	I	I	A	L	S	K
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 3msw chain A Region: 27 - 51 Aligned: 25 Modelled: 25 Confidence: 29.2% Identity: 24% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a protein with unknown function (bf3112) from2 bacteroides fragilis nctc 9343 at 1.90 a resolution Phyre2 PDB 1s6l chain A domain 1 Region: 26 - 34 Aligned: 9 Modelled: 9 Confidence: 17.4% Identity: 33% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: MerB N-terminal domain-like Phyre2 PDB 3m3g chain A Region: 25 - 63 Aligned: 39 Modelled: 39 Confidence: 17.3% Identity: 44% PDB header:polysaccharide-binding protein Chain: A: PDB Molecule:epl1 protein; PDBTitle: crystal structure of sm1, an elicitor of plant defence responses from2 trichoderma virens. Phyre2 PDB 2yvz chain A Region: 19 - 34 Aligned: 16 Modelled: 16 Confidence: 14.3% Identity: 50% PDB header:transport protein Chain: A: PDB Molecule:mg2+ transporter mgte; PDBTitle: crystal structure of magnesium transporter mgte cytosolic domain,2 mg2+-free form Phyre2 PDB 3kxr chain A Region: 19 - 34 Aligned: 16 Modelled: 16 Confidence: 13.5% Identity: 38% PDB header:transport protein Chain: A: PDB Molecule:magnesium transporter, putative; PDBTitle: structure of the cystathionine beta-synthase pair domain of the2 putative mg2+ transporter so5017 from shewanella oneidensis mr-1. Phyre2 PDB 2yzq chain A domain 1 Region: 9 - 34 Aligned: 26 Modelled: 26 Confidence: 13.2% Identity: 19% Fold: CBS-domain pair Superfamily: CBS-domain pair Family: CBS-domain pair Phyre2 PDB 2yzq chain A domain 2 Region: 19 - 34 Aligned: 16 Modelled: 16 Confidence: 12.2% Identity: 38% Fold: CBS-domain pair Superfamily: CBS-domain pair Family: CBS-domain pair Phyre2 PDB 3gvz chain B Region: 17 - 39 Aligned: 23 Modelled: 23 Confidence: 12.1% Identity: 22% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein cv2077; PDBTitle: crystal structure of the protein cv2077 from2 chromobacterium violaceum. northeast structural genomics3 consortium target cvr62 Phyre2 PDB 2oux chain B Region: 19 - 34 Aligned: 16 Modelled: 16 Confidence: 12.0% Identity: 38% PDB header:transport protein Chain: B: PDB Molecule:magnesium transporter; PDBTitle: crystal structure of the soluble part of a magnesium transporter Phyre2 PDB 2oox chain E domain 1 Region: 9 - 34 Aligned: 26 Modelled: 26 Confidence: 11.0% Identity: 15% Fold: CBS-domain pair Superfamily: CBS-domain pair Family: CBS-domain pair Phyre2 PDB 2pdt chain D Region: 25 - 35 Aligned: 11 Modelled: 11 Confidence: 10.8% Identity: 36% PDB header:circadian clock protein Chain: D: PDB Molecule:vivid pas protein vvd; PDBTitle: 2.3 angstrom structure of phosphodiesterase treated vivid Phyre2 PDB 1p0z chain A Region: 24 - 34 Aligned: 11 Modelled: 11 Confidence: 10.5% Identity: 27% Fold: Profilin-like Superfamily: Sensory domain-like Family: Sensory domain of two-component sensor kinase Phyre2 PDB 1e6y chain B domain 2 Region: 21 - 37 Aligned: 17 Modelled: 17 Confidence: 10.0% Identity: 47% Fold: Ferredoxin-like Superfamily: Methyl-coenzyme M reductase subunits Family: Methyl-coenzyme M reductase alpha and beta chain N-terminal domain Phyre2 PDB 2bba chain A domain 1 Region: 24 - 59 Aligned: 36 Modelled: 36 Confidence: 9.8% Identity: 22% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Ephrin receptor ligand binding domain Phyre2 PDB 2yvx chain D Region: 19 - 34 Aligned: 16 Modelled: 16 Confidence: 9.4% Identity: 50% PDB header:transport protein Chain: D: PDB Molecule:mg2+ transporter mgte; PDBTitle: crystal structure of magnesium transporter mgte Phyre2 PDB 1vr9 chain B Region: 19 - 34 Aligned: 16 Modelled: 16 Confidence: 8.3% Identity: 44% PDB header:unknown function Chain: B: PDB Molecule:cbs domain protein/act domain protein; PDBTitle: crystal structure of a cbs domain pair/act domain protein (tm0892)2 from thermotoga maritima at 1.70 a resolution Phyre2 PDB 1vr9 chain A domain 3 Region: 19 - 34 Aligned: 16 Modelled: 16 Confidence: 8.3% Identity: 44% Fold: CBS-domain pair Superfamily: CBS-domain pair Family: CBS-domain pair Phyre2 PDB 3fna chain A Region: 19 - 34 Aligned: 16 Modelled: 12 Confidence: 7.9% Identity: 13% PDB header:isomerase Chain: A: PDB Molecule:possible arabinose 5-phosphate isomerase; PDBTitle: crystal structure of the cbs pair of possible d-arabinose 5-phosphate2 isomerase yrbh from escherichia coli cft073 Phyre2 PDB 3kpb chain A Region: 9 - 34 Aligned: 26 Modelled: 26 Confidence: 7.5% Identity: 27% PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein mj0100; PDBTitle: crystal structure of the cbs domain pair of protein mj01002 in complex with 5 -methylthioadenosine and s-adenosyl-l-3 methionine. Phyre2 PDB 2oux chain A domain 2 Region: 9 - 34 Aligned: 26 Modelled: 26 Confidence: 7.1% Identity: 23% Fold: CBS-domain pair Superfamily: CBS-domain pair Family: CBS-domain pair Phyre2 1 c3mswA_ 2 d1s6la1 3 c3m3gA_ 4 c2yvzA_ 5 c3kxrA_ 6 d2yzqa1 7 d2yzqa2 8 c3gvzB_ 9 c2ouxB_ 10 d2ooxe1 11 c2pdtD_ 12 d1p0za_ 13 d1e6yb2 14 d2bbaa1 15 c2yvxD_ 16 c1vr9B_ 17 d1vr9a3 18 c3fnaA_ 19 c3kpbA_ 20 d2ouxa2 21 22 23 24 25 26 27 28 29 30 31 32

Detailed template information

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

1 c3mswA_ 29.2 24 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a protein with unknown function (bf3112) from2 bacteroides fragilis nctc 9343 at 1.90 a resolution 2 d1s6la1 17.4 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MerB N-terminal domain-like 3 c3m3gA_ 17.3 44 PDB header:polysaccharide-binding protein Chain: A: PDB Molecule:epl1 protein; PDBTitle: crystal structure of sm1, an elicitor of plant defence responses from2 trichoderma virens. 4 c2yvzA_ 14.3 50 PDB header:transport protein Chain: A: PDB Molecule:mg2+ transporter mgte; PDBTitle: crystal structure of magnesium transporter mgte cytosolic domain,2 mg2+-free form 5 c3kxrA_ 13.5 38 PDB header:transport protein Chain: A: PDB Molecule:magnesium transporter, putative; PDBTitle: structure of the cystathionine beta-synthase pair domain of the2 putative mg2+ transporter so5017 from shewanella oneidensis mr-1. 6 d2yzqa1 13.2 19 Fold:CBS-domain pair Superfamily:CBS-domain pair Family:CBS-domain pair 7 d2yzqa2 12.2 38 Fold:CBS-domain pair Superfamily:CBS-domain pair Family:CBS-domain pair 8 c3gvzB_ 12.1 22 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein cv2077; PDBTitle: crystal structure of the protein cv2077 from2 chromobacterium violaceum. northeast structural genomics3 consortium target cvr62 9 c2ouxB_ 12.0 38 PDB header:transport protein Chain: B: PDB Molecule:magnesium transporter; PDBTitle: crystal structure of the soluble part of a magnesium transporter 10 d2ooxe1 11.0 15 Fold:CBS-domain pair Superfamily:CBS-domain pair Family:CBS-domain pair 11 c2pdtD_ 10.8 36 PDB header:circadian clock protein Chain: D: PDB Molecule:vivid pas protein vvd; PDBTitle: 2.3 angstrom structure of phosphodiesterase treated vivid 12 d1p0za_ 10.5 27 Fold:Profilin-like Superfamily:Sensory domain-like Family:Sensory domain of two-component sensor kinase 13 d1e6yb2 10.0 47 Fold:Ferredoxin-like Superfamily:Methyl-coenzyme M reductase subunits Family:Methyl-coenzyme M reductase alpha and beta chain N-terminal domain 14 d2bbaa1 9.8 22 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Ephrin receptor ligand binding domain 15 c2yvxD_ 9.4 50 PDB header:transport protein Chain: D: PDB Molecule:mg2+ transporter mgte; PDBTitle: crystal structure of magnesium transporter mgte 16 c1vr9B_ 8.3 44 PDB header:unknown function Chain: B: PDB Molecule:cbs domain protein/act domain protein; PDBTitle: crystal structure of a cbs domain pair/act domain protein (tm0892)2 from thermotoga maritima at 1.70 a resolution 17 d1vr9a3 8.3 44 Fold:CBS-domain pair Superfamily:CBS-domain pair Family:CBS-domain pair 18 c3fnaA_ 7.9 13 PDB header:isomerase Chain: A: PDB Molecule:possible arabinose 5-phosphate isomerase; PDBTitle: crystal structure of the cbs pair of possible d-arabinose 5-phosphate2 isomerase yrbh from escherichia coli cft073 19 c3kpbA_ 7.5 27 PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein mj0100; PDBTitle: crystal structure of the cbs domain pair of protein mj01002 in complex with 5 -methylthioadenosine and s-adenosyl-l-3 methionine. 20 d2ouxa2 7.1 23 Fold:CBS-domain pair Superfamily:CBS-domain pair Family:CBS-domain pair 21 d1bywa_ not modelled 7.0 31 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Flavin-binding PAS domain 22 c2qbxB_ not modelled 6.8 28 PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-b receptor 2; PDBTitle: ephb2/snew antagonistic peptide complex 23 c2p9mD_ not modelled 6.7 25 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:hypothetical protein mj0922; PDBTitle: crystal structure of conserved hypothetical protein mj0922 from2 methanocaldococcus jannaschii dsm 2661 24 d3ddja1 not modelled 6.4 0 Fold:CBS-domain pair Superfamily:CBS-domain pair Family:CBS-domain pair 25 d1pvma4 not modelled 6.0 23 Fold:CBS-domain pair Superfamily:CBS-domain pair Family:CBS-domain pair 26 d1oqva_ not modelled 5.8 42 Fold:Pili subunits Superfamily:Pili subunits Family:TcpA-like pilin 27 d1jnua_ not modelled 5.6 15 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Flavin-binding PAS domain 28 d1jcna4 not modelled 5.6 26 Fold:CBS-domain pair Superfamily:CBS-domain pair Family:CBS-domain pair 29 d2v8qe1 not modelled 5.5 12 Fold:CBS-domain pair Superfamily:CBS-domain pair Family:CBS-domain pair 30 d2ef7a1 not modelled 5.5 31 Fold:CBS-domain pair Superfamily:CBS-domain pair Family:CBS-domain pair 31 d2riha1 not modelled 5.3 27 Fold:CBS-domain pair Superfamily:CBS-domain pair Family:CBS-domain pair 32 c2v8kA_ not modelled 5.1 29 PDB header:lyase Chain: A: PDB Molecule:pectate lyase; PDBTitle: structure of a family 2 pectate lyase in complex with2 trigalacturonic acid

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