Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	K	S	W	W	A	E	K	S	T	S	E	K	Q	I	V	A	A	L	A	V	L	S	L	G	V	F	C	W	L	G	V	I	K	P	I	D	T	Y	I	A	E	H	Q	S	H	A	Q	K	I	K	K	D	I	K	W	M	Q	D
Secondary structure
SS confidence
Disorder		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Q	A	S	T	H	G	L	L	G	H	P	A	L	T	Q	P	I	K	N	I	L	L	E	E	A	K	R	E	N	L	A	I	T	L	E	N	G	P	D	N	T	L	T	I	H	P	V	T	A	P	L	E	N	V	S	R	W	L	T	T
Secondary structure
SS confidence
Disorder							?	?	?	?	?	?	?	?	?	?	?												?	?							?	?	?		?										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.
Sequence		A	Q	V	T	Y	G	I	V	I	E	D	L	Q	F	T	L	A	G	N	E	E	I	T	L	R	H	L	S	F	R	E	Q	Q
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 1uv7 chain A Region: 75 - 149 Aligned: 71 Modelled: 75 Confidence: 99.8% Identity: 11% PDB header:transport Chain: A: PDB Molecule:general secretion pathway protein m; PDBTitle: periplasmic domain of epsm from vibrio cholerae Phyre2 PDB 1uv7 chain A Region: 75 - 149 Aligned: 71 Modelled: 75 Confidence: 99.8% Identity: 11% Fold: RRF/tRNA synthetase additional domain-like Superfamily: General secretion pathway protein M, EpsM Family: General secretion pathway protein M, EpsM Phyre2 PDB 2rjz chain A Region: 48 - 149 Aligned: 101 Modelled: 102 Confidence: 97.7% Identity: 9% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:pilo protein; PDBTitle: crystal structure of the type 4 fimbrial biogenesis protein pilo from2 pseudomonas aeruginosa Phyre2 PDB 2rdd chain B Region: 18 - 46 Aligned: 29 Modelled: 29 Confidence: 57.7% Identity: 17% PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. Phyre2 PDB 2y9k chain G Region: 74 - 152 Aligned: 78 Modelled: 79 Confidence: 47.2% Identity: 9% PDB header:protein transport Chain: G: PDB Molecule:protein invg; PDBTitle: three-dimensional model of salmonella's needle complex at2 subnanometer resolution Phyre2 PDB 1bjn chain A Region: 73 - 126 Aligned: 54 Modelled: 54 Confidence: 29.5% Identity: 9% Fold: PLP-dependent transferase-like Superfamily: PLP-dependent transferases Family: GABA-aminotransferase-like Phyre2 PDB 3gr5 chain A Region: 74 - 151 Aligned: 77 Modelled: 78 Confidence: 28.1% Identity: 10% PDB header:membrane protein Chain: A: PDB Molecule:escc; PDBTitle: periplasmic domain of the outer membrane secretin escc from2 enteropathogenic e.coli (epec) Phyre2 PDB 1ppj chain C domain 2 Region: 1 - 36 Aligned: 35 Modelled: 36 Confidence: 26.1% Identity: 9% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1tp6 chain A Region: 110 - 153 Aligned: 41 Modelled: 44 Confidence: 24.9% Identity: 22% Fold: Cystatin-like Superfamily: NTF2-like Family: PA1314-like Phyre2 PDB 1dnl chain A Region: 106 - 146 Aligned: 41 Modelled: 41 Confidence: 24.9% Identity: 15% Fold: Split barrel-like Superfamily: FMN-binding split barrel Family: PNP-oxidase like Phyre2 PDB 3hd7 chain A Region: 3 - 34 Aligned: 27 Modelled: 27 Confidence: 22.9% Identity: 22% PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 Phyre2 PDB 1yio chain A domain 1 Region: 2 - 21 Aligned: 20 Modelled: 20 Confidence: 21.4% Identity: 10% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 2c0r chain A domain 1 Region: 73 - 126 Aligned: 54 Modelled: 54 Confidence: 20.2% Identity: 7% Fold: PLP-dependent transferase-like Superfamily: PLP-dependent transferases Family: GABA-aminotransferase-like Phyre2 PDB 1x4p chain A domain 1 Region: 8 - 18 Aligned: 11 Modelled: 11 Confidence: 18.6% Identity: 18% Fold: Surp module (SWAP domain) Superfamily: Surp module (SWAP domain) Family: Surp module (SWAP domain) Phyre2 PDB 1nrg chain A Region: 110 - 147 Aligned: 38 Modelled: 38 Confidence: 18.1% Identity: 11% Fold: Split barrel-like Superfamily: FMN-binding split barrel Family: PNP-oxidase like Phyre2 PDB 1nrg chain A Region: 110 - 147 Aligned: 38 Modelled: 38 Confidence: 18.1% Identity: 11% PDB header:oxidoreductase Chain: A: PDB Molecule:pyridoxine 5'-phosphate oxidase; PDBTitle: structure and properties of recombinant human pyridoxine-5'-phosphate2 oxidase Phyre2 PDB 1t9m chain A Region: 106 - 147 Aligned: 42 Modelled: 42 Confidence: 17.1% Identity: 17% Fold: Split barrel-like Superfamily: FMN-binding split barrel Family: PNP-oxidase like Phyre2 PDB 2knc chain A Region: 15 - 34 Aligned: 20 Modelled: 20 Confidence: 16.5% Identity: 25% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1hyw chain A Region: 89 - 127 Aligned: 37 Modelled: 39 Confidence: 14.4% Identity: 5% Fold: gpW/XkdW-like Superfamily: Head-to-tail joining protein W, gpW Family: Head-to-tail joining protein W, gpW Phyre2 PDB 1bcc chain C domain 3 Region: 1 - 36 Aligned: 35 Modelled: 36 Confidence: 12.8% 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 1 c1uv7A_ 2 d1uv7a_ 3 c2rjzA_ 4 c2rddB_ 5 c2y9kG_ 6 d1bjna_ 7 c3gr5A_ 8 d1ppjc2 9 d1tp6a_ 10 d1dnla_ 11 c3hd7A_ 12 d1yioa1 13 d2c0ra1 14 d1x4pa1 15 d1nrga_ 16 c1nrgA_ 17 d1t9ma_ 18 c2kncA_ 19 d1hywa_ 20 d1bccc3 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72

Detailed template information

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

1 c1uv7A_ 99.8 11 PDB header:transport Chain: A: PDB Molecule:general secretion pathway protein m; PDBTitle: periplasmic domain of epsm from vibrio cholerae 2 d1uv7a_ 99.8 11 Fold:RRF/tRNA synthetase additional domain-like Superfamily:General secretion pathway protein M, EpsM Family:General secretion pathway protein M, EpsM 3 c2rjzA_ 97.7 9 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:pilo protein; PDBTitle: crystal structure of the type 4 fimbrial biogenesis protein pilo from2 pseudomonas aeruginosa 4 c2rddB_ 57.7 17 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. 5 c2y9kG_ 47.2 9 PDB header:protein transport Chain: G: PDB Molecule:protein invg; PDBTitle: three-dimensional model of salmonella's needle complex at2 subnanometer resolution 6 d1bjna_ 29.5 9 Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:GABA-aminotransferase-like 7 c3gr5A_ 28.1 10 PDB header:membrane protein Chain: A: PDB Molecule:escc; PDBTitle: periplasmic domain of the outer membrane secretin escc from2 enteropathogenic e.coli (epec) 8 d1ppjc2 26.1 9 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 9 d1tp6a_ 24.9 22 Fold:Cystatin-like Superfamily:NTF2-like Family:PA1314-like 10 d1dnla_ 24.9 15 Fold:Split barrel-like Superfamily:FMN-binding split barrel Family:PNP-oxidase like 11 c3hd7A_ 22.9 22 PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 12 d1yioa1 21.4 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 13 d2c0ra1 20.2 7 Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:GABA-aminotransferase-like 14 d1x4pa1 18.6 18 Fold:Surp module (SWAP domain) Superfamily:Surp module (SWAP domain) Family:Surp module (SWAP domain) 15 d1nrga_ 18.1 11 Fold:Split barrel-like Superfamily:FMN-binding split barrel Family:PNP-oxidase like 16 c1nrgA_ 18.1 11 PDB header:oxidoreductase Chain: A: PDB Molecule:pyridoxine 5'-phosphate oxidase; PDBTitle: structure and properties of recombinant human pyridoxine-5'-phosphate2 oxidase 17 d1t9ma_ 17.1 17 Fold:Split barrel-like Superfamily:FMN-binding split barrel Family:PNP-oxidase like 18 c2kncA_ 16.5 25 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 19 d1hywa_ 14.4 5 Fold:gpW/XkdW-like Superfamily:Head-to-tail joining protein W, gpW Family:Head-to-tail joining protein W, gpW 20 d1bccc3 12.8 11 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 21 d1v54d_ not modelled 12.5 27 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit IV Family:Mitochondrial cytochrome c oxidase subunit IV 22 c3mn7S_ not modelled 12.1 20 PDB header:contractile protein/protein binding Chain: S: PDB Molecule:spire ddd; PDBTitle: structures of actin-bound wh2 domains of spire and the implication for2 filament nucleation 23 c2rnjA_ not modelled 11.8 19 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 24 c3mn5S_ not modelled 11.8 20 PDB header:contractile protein/protein binding Chain: S: PDB Molecule:protein spire; PDBTitle: structures of actin-bound wh2 domains of spire and the implication for2 filament nucleation 25 c3qm2A_ not modelled 11.4 9 PDB header:transferase Chain: A: PDB Molecule:phosphoserine aminotransferase; PDBTitle: 2.25 angstrom crystal structure of phosphoserine aminotransferase2 (serc) from salmonella enterica subsp. enterica serovar typhimurium 26 c2d89A_ not modelled 10.7 19 PDB header:structural protein, protein binding Chain: A: PDB Molecule:ehbp1 protein; PDBTitle: solution structure of the ch domain from human eh domain2 binding protein 1 27 c2y69Q_ not modelled 10.6 27 PDB header:electron transport Chain: Q: PDB Molecule:cytochrome c oxidase subunit 4 isoform 1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 28 c2w7vB_ not modelled 10.5 11 PDB header:transport protein Chain: B: PDB Molecule:general secretion pathway protein l; PDBTitle: periplasmic domain of epsl from vibrio parahaemolyticus 29 d2csua2 not modelled 10.4 7 Fold:Flavodoxin-like Superfamily:Succinyl-CoA synthetase domains Family:Succinyl-CoA synthetase domains 30 c2d88A_ not modelled 10.3 24 PDB header:signaling protein, protein binding Chain: A: PDB Molecule:protein mical-3; PDBTitle: solution structure of the ch domain from human mical-32 protein 31 d1ty9a_ not modelled 10.0 14 Fold:Split barrel-like Superfamily:FMN-binding split barrel Family:PNP-oxidase like 32 d2p8ia1 not modelled 9.4 14 Fold:Ferredoxin-like Superfamily:DOPA-like Family:DOPA dioxygenase-like 33 c2yv2A_ not modelled 9.2 9 PDB header:ligase Chain: A: PDB Molecule:succinyl-coa synthetase alpha chain; PDBTitle: crystal structure of succinyl-coa synthetase alpha chain from2 aeropyrum pernix k1 34 c3adyA_ not modelled 8.9 16 PDB header:proton transport Chain: A: PDB Molecule:dotd; PDBTitle: crystal structure of dotd from legionella 35 d1dwka2 not modelled 8.8 13 Fold:Cyanase C-terminal domain Superfamily:Cyanase C-terminal domain Family:Cyanase C-terminal domain 36 c2k1aA_ not modelled 8.8 29 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment 37 d2f06a2 not modelled 8.6 15 Fold:Ferredoxin-like Superfamily:ACT-like Family:BT0572-like 38 c2iv1J_ not modelled 8.5 13 PDB header:lyase Chain: J: PDB Molecule:cyanate hydratase; PDBTitle: site directed mutagenesis of key residues involved in the2 catalytic mechanism of cyanase 39 d1dxxa2 not modelled 8.4 10 Fold:CH domain-like Superfamily:Calponin-homology domain, CH-domain Family:Calponin-homology domain, CH-domain 40 d1sh5a2 not modelled 8.3 19 Fold:CH domain-like Superfamily:Calponin-homology domain, CH-domain Family:Calponin-homology domain, CH-domain 41 c1wylA_ not modelled 8.3 30 PDB header:signaling protein Chain: A: PDB Molecule:nedd9 interacting protein with calponin homology PDBTitle: solution structure of the ch domain of human nedd92 interacting protein with calponin homology and lim domains 42 d2a2ja1 not modelled 8.2 15 Fold:Split barrel-like Superfamily:FMN-binding split barrel Family:PNP-oxidase like 43 c2kncB_ not modelled 7.9 14 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 44 c1x3uA_ not modelled 7.7 26 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulatory protein fixj; PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot 45 c2a2jA_ not modelled 7.6 15 PDB header:oxidoreductase Chain: A: PDB Molecule:pyridoxamine 5'-phosphate oxidase; PDBTitle: crystal structure of a putative pyridoxine 5'-phosphate oxidase2 (rv2607) from mycobacterium tuberculosis 46 d1ku3a_ not modelled 7.6 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 47 c2pebB_ not modelled 7.4 10 PDB header:oxidoreductase Chain: B: PDB Molecule:putative dioxygenase; PDBTitle: crystal structure of a putative dioxygenase (npun_f1925) from nostoc2 punctiforme pcc 73102 at 1.46 a resolution 48 d3e9va1 not modelled 7.4 14 Fold:BTG domain-like Superfamily:BTG domain-like Family:BTG domain-like 49 c2d87A_ not modelled 7.2 15 PDB header:structural protein, protein binding Chain: A: PDB Molecule:smoothelin splice isoform l2; PDBTitle: solution structure of the ch domain from human smoothelin2 splice isoform l2 50 d1wb9a4 not modelled 7.2 13 Fold:MutS N-terminal domain-like Superfamily:DNA repair protein MutS, domain I Family:DNA repair protein MutS, domain I 51 c3smtA_ not modelled 7.2 19 PDB header:transferase Chain: A: PDB Molecule:histone-lysine n-methyltransferase setd3; PDBTitle: crystal structure of human set domain-containing protein3 52 d1bkra_ not modelled 7.2 15 Fold:CH domain-like Superfamily:Calponin-homology domain, CH-domain Family:Calponin-homology domain, CH-domain 53 d1ewqa4 not modelled 7.1 18 Fold:MutS N-terminal domain-like Superfamily:DNA repair protein MutS, domain I Family:DNA repair protein MutS, domain I 54 c3cwbC_ not modelled 6.8 11 PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome b; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d 55 d2z15a1 not modelled 6.8 14 Fold:BTG domain-like Superfamily:BTG domain-like Family:BTG domain-like 56 c3hilB_ not modelled 6.7 38 PDB header:transferase Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: sam domain of human ephrin type-a receptor 1 (epha1) 57 d3dhxa1 not modelled 6.5 22 Fold:Ferredoxin-like Superfamily:ACT-like Family:NIL domain-like 58 d1ygya3 not modelled 6.5 12 Fold:Ferredoxin-like Superfamily:ACT-like Family:Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain 59 d2af7a1 not modelled 6.3 6 Fold:AhpD-like Superfamily:AhpD-like Family:CMD-like 60 c2ogfD_ not modelled 6.2 12 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 61 d1ulra_ not modelled 6.2 17 Fold:Ferredoxin-like Superfamily:Acylphosphatase/BLUF domain-like Family:Acylphosphatase-like 62 c3f6oB_ not modelled 5.9 18 PDB header:transcription regulator Chain: B: PDB Molecule:probable transcriptional regulator, arsr family PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566 63 d2iw0a1 not modelled 5.9 6 Fold:7-stranded beta/alpha barrel Superfamily:Glycoside hydrolase/deacetylase Family:NodB-like polysaccharide deacetylase 64 c2d1uA_ not modelled 5.8 10 PDB header:metal transport Chain: A: PDB Molecule:iron(iii) dicitrate transport protein feca; PDBTitle: solution strcuture of the periplasmic signaling domain of2 feca from escherichia coli 65 d1ku7a_ not modelled 5.6 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 66 c3mgjA_ not modelled 5.6 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein mj1480; PDBTitle: crystal structure of the saccharop_dh_n domain of mj14802 protein from methanococcus jannaschii. northeast structural3 genomics consortium target mjr83a. 67 c3dmyA_ not modelled 5.6 10 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein fdra; PDBTitle: crystal structure of a predicated acyl-coa synthetase from e.coli 68 c2e8nA_ not modelled 5.4 33 PDB header:transferase, signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 2; PDBTitle: solution structure of the c-terminal sam-domain of ephaa2:2 ephrin type-a receptor 2 precursor (ec 2.7.10.1) 69 d1euca2 not modelled 5.2 11 Fold:Flavodoxin-like Superfamily:Succinyl-CoA synthetase domains Family:Succinyl-CoA synthetase domains 70 c2yh5A_ not modelled 5.1 25 PDB header:lipid binding protein Chain: A: PDB Molecule:dapx protein; PDBTitle: structure of the c-terminal domain of bamc 71 c1zzvA_ not modelled 5.1 10 PDB header:membrane protein, metal transport Chain: A: PDB Molecule:iron(iii) dicitrate transport protein feca; PDBTitle: solution nmr structure of the periplasmic signaling domain2 of the outer membrane iron transporter feca from3 escherichia coli. 72 d1bhda_ not modelled 5.0 10 Fold:CH domain-like Superfamily:Calponin-homology domain, CH-domain Family:Calponin-homology domain, CH-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

---

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