Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	R	D	K	F	I	H	Y	F	Q	Q	W	R	E	R	Q	L	S	R	G	E	H	W	L	A	Q	H	L	A	G	R	S	P	R	E	K	G	M	L	L	A	A	V	V	F	L	F	S	V	G	Y	Y	V	L	I	W	Q	P	L
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	E	R	I	E	Q	Q	E	T	I	L	Q	Q	L	V	A	M	N	T	R	L	K	N	A	A	P	D	I	I	A	A	R	K	S	A	T	T	T	P	A	Q	V	S	R	V	I	S	D	S	A	S	A	H	S	V	V	I	R	R	I
Secondary structure
SS confidence
Disorder																															?	?	?	?	?	?	?	?	?	?	?	?												?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.
Sequence		A	D	R	G	E	N	I	Q	V	W	I	E	P	V	V	F	N	D	L	L	K	W	L	N	A	L	D	E	K	Y	A	L	R	V	T	Q	I	D	V	S	A	A	E	K	P	G	M	V	N	V	Q	R	L	E	F	G	R	G
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: 100 - 178 Aligned: 75 Modelled: 79 Confidence: 99.9% Identity: 36% 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: 100 - 178 Aligned: 75 Modelled: 79 Confidence: 99.9% Identity: 36% 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: 60 - 176 Aligned: 115 Modelled: 117 Confidence: 97.7% Identity: 10% 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: 39 - 69 Aligned: 31 Modelled: 31 Confidence: 60.1% Identity: 23% 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 1v54 chain D Region: 10 - 58 Aligned: 41 Modelled: 49 Confidence: 53.7% Identity: 24% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit IV Family: Mitochondrial cytochrome c oxidase subunit IV Phyre2 PDB 2y69 chain Q Region: 10 - 58 Aligned: 41 Modelled: 49 Confidence: 49.0% Identity: 24% 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 Phyre2 PDB 1yio chain A domain 1 Region: 21 - 44 Aligned: 24 Modelled: 24 Confidence: 44.6% Identity: 21% 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 1ppj chain C domain 2 Region: 32 - 63 Aligned: 31 Modelled: 32 Confidence: 24.0% Identity: 3% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1t9m chain A Region: 131 - 175 Aligned: 45 Modelled: 45 Confidence: 23.4% Identity: 9% Fold: Split barrel-like Superfamily: FMN-binding split barrel Family: PNP-oxidase like Phyre2 PDB 2y9k chain G Region: 99 - 146 Aligned: 48 Modelled: 48 Confidence: 20.3% Identity: 15% PDB header:protein transport Chain: G: PDB Molecule:protein invg; PDBTitle: three-dimensional model of salmonella's needle complex at2 subnanometer resolution Phyre2 PDB 1gt0 chain D Region: 6 - 37 Aligned: 32 Modelled: 32 Confidence: 19.2% Identity: 22% Fold: HMG-box Superfamily: HMG-box Family: HMG-box Phyre2 PDB 1bjn chain A Region: 98 - 151 Aligned: 54 Modelled: 54 Confidence: 18.9% Identity: 6% Fold: PLP-dependent transferase-like Superfamily: PLP-dependent transferases Family: GABA-aminotransferase-like Phyre2 PDB 1x4p chain A domain 1 Region: 31 - 41 Aligned: 11 Modelled: 11 Confidence: 18.3% Identity: 36% Fold: Surp module (SWAP domain) Superfamily: Surp module (SWAP domain) Family: Surp module (SWAP domain) Phyre2 PDB 1ulr chain A Region: 103 - 167 Aligned: 64 Modelled: 65 Confidence: 17.4% Identity: 17% Fold: Ferredoxin-like Superfamily: Acylphosphatase/BLUF domain-like Family: Acylphosphatase-like Phyre2 PDB 1k99 chain A Region: 6 - 37 Aligned: 32 Modelled: 32 Confidence: 17.0% Identity: 13% Fold: HMG-box Superfamily: HMG-box Family: HMG-box Phyre2 PDB 2co9 chain A Region: 6 - 37 Aligned: 32 Modelled: 32 Confidence: 16.6% Identity: 13% PDB header:transcription Chain: A: PDB Molecule:thymus high mobility group box protein tox; PDBTitle: solution structure of the hmg_box domain of thymus high2 mobility group box protein tox from mouse Phyre2 PDB 1ty9 chain A Region: 131 - 175 Aligned: 45 Modelled: 45 Confidence: 16.1% Identity: 11% Fold: Split barrel-like Superfamily: FMN-binding split barrel Family: PNP-oxidase like Phyre2 PDB 1bcc chain C domain 3 Region: 32 - 63 Aligned: 31 Modelled: 32 Confidence: 15.0% Identity: 6% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 2jsx chain A Region: 99 - 157 Aligned: 59 Modelled: 59 Confidence: 14.0% Identity: 7% PDB header:chaperone Chain: A: PDB Molecule:protein napd; PDBTitle: solution structure of the e. coli tat proofreading2 chaperone protein napd Phyre2 PDB 2yul chain A Region: 6 - 37 Aligned: 32 Modelled: 32 Confidence: 13.3% Identity: 19% PDB header:transcription Chain: A: PDB Molecule:transcription factor sox-17; PDBTitle: solution structure of the hmg box of human transcription2 factor sox-17 Phyre2 1 c1uv7A_ 2 d1uv7a_ 3 c2rjzA_ 4 c2rddB_ 5 d1v54d_ 6 c2y69Q_ 7 d1yioa1 8 d1ppjc2 9 d1t9ma_ 10 c2y9kG_ 11 d1gt0d_ 12 d1bjna_ 13 d1x4pa1 14 d1ulra_ 15 d1k99a_ 16 c2co9A_ 17 d1ty9a_ 18 d1bccc3 19 c2jsxA_ 20 c2yulA_ 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

Detailed template information

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

1 c1uv7A_ 99.9 36 PDB header:transport Chain: A: PDB Molecule:general secretion pathway protein m; PDBTitle: periplasmic domain of epsm from vibrio cholerae 2 d1uv7a_ 99.9 36 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 10 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_ 60.1 23 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 d1v54d_ 53.7 24 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit IV Family:Mitochondrial cytochrome c oxidase subunit IV 6 c2y69Q_ 49.0 24 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 7 d1yioa1 44.6 21 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) 8 d1ppjc2 24.0 3 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 9 d1t9ma_ 23.4 9 Fold:Split barrel-like Superfamily:FMN-binding split barrel Family:PNP-oxidase like 10 c2y9kG_ 20.3 15 PDB header:protein transport Chain: G: PDB Molecule:protein invg; PDBTitle: three-dimensional model of salmonella's needle complex at2 subnanometer resolution 11 d1gt0d_ 19.2 22 Fold:HMG-box Superfamily:HMG-box Family:HMG-box 12 d1bjna_ 18.9 6 Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:GABA-aminotransferase-like 13 d1x4pa1 18.3 36 Fold:Surp module (SWAP domain) Superfamily:Surp module (SWAP domain) Family:Surp module (SWAP domain) 14 d1ulra_ 17.4 17 Fold:Ferredoxin-like Superfamily:Acylphosphatase/BLUF domain-like Family:Acylphosphatase-like 15 d1k99a_ 17.0 13 Fold:HMG-box Superfamily:HMG-box Family:HMG-box 16 c2co9A_ 16.6 13 PDB header:transcription Chain: A: PDB Molecule:thymus high mobility group box protein tox; PDBTitle: solution structure of the hmg_box domain of thymus high2 mobility group box protein tox from mouse 17 d1ty9a_ 16.1 11 Fold:Split barrel-like Superfamily:FMN-binding split barrel Family:PNP-oxidase like 18 d1bccc3 15.0 6 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 19 c2jsxA_ 14.0 7 PDB header:chaperone Chain: A: PDB Molecule:protein napd; PDBTitle: solution structure of the e. coli tat proofreading2 chaperone protein napd 20 c2yulA_ 13.3 19 PDB header:transcription Chain: A: PDB Molecule:transcription factor sox-17; PDBTitle: solution structure of the hmg box of human transcription2 factor sox-17 21 c2eefA_ not modelled 12.2 24 PDB header:sugar binding protein Chain: A: PDB Molecule:protein phosphatase 1, regulatory (inhibitor) PDBTitle: solution structure of the cbm_21 domain from human protein2 phosphatase 1, regulatory (inhibitor) subunit 3b 22 d1hywa_ not modelled 11.4 16 Fold:gpW/XkdW-like Superfamily:Head-to-tail joining protein W, gpW Family:Head-to-tail joining protein W, gpW 23 c2rnjA_ not modelled 11.3 25 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 24 c2cs1A_ not modelled 11.2 19 PDB header:dna binding protein Chain: A: PDB Molecule:pms1 protein homolog 1; PDBTitle: solution structure of the hmg domain of human dna mismatch2 repair protein 25 c3cwbC_ not modelled 11.1 6 PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome b; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d 26 c2kncA_ not modelled 11.1 10 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 27 c3mn7S_ not modelled 10.7 50 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 28 c3mn5S_ not modelled 10.4 50 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 29 d1wgfa_ not modelled 10.3 22 Fold:HMG-box Superfamily:HMG-box Family:HMG-box 30 c1x3uA_ not modelled 10.2 35 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 31 c3gr5A_ not modelled 10.1 15 PDB header:membrane protein Chain: A: PDB Molecule:escc; PDBTitle: periplasmic domain of the outer membrane secretin escc from2 enteropathogenic e.coli (epec) 32 c2k4yA_ not modelled 9.9 6 PDB header:metal transport Chain: A: PDB Molecule:feoa-like protein; PDBTitle: nmr structure of feoa-like protein from clostridium2 acetobutylicum: northeast structural genomics consortium3 target car178 33 c1wz6A_ not modelled 9.8 31 PDB header:transcription Chain: A: PDB Molecule:hmg-box transcription factor bbx; PDBTitle: solution structure of the hmg_box domain of murine bobby2 sox homolog 34 d1w2ia_ not modelled 9.8 13 Fold:Ferredoxin-like Superfamily:Acylphosphatase/BLUF domain-like Family:Acylphosphatase-like 35 d1b7yb4 not modelled 9.8 13 Fold:Ferredoxin-like Superfamily:Anticodon-binding domain of PheRS Family:Anticodon-binding domain of PheRS 36 d2c0ra1 not modelled 9.0 6 Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:GABA-aminotransferase-like 37 c2w7vB_ not modelled 7.7 13 PDB header:transport protein Chain: B: PDB Molecule:general secretion pathway protein l; PDBTitle: periplasmic domain of epsl from vibrio parahaemolyticus 38 c1peiA_ not modelled 7.7 36 PDB header:nucleotidyltransferase Chain: A: PDB Molecule:pepc22; PDBTitle: nmr structure of the membrane-binding domain of ctp2 phosphocholine cytidylyltransferase, 10 structures 39 d1j46a_ not modelled 7.7 24 Fold:HMG-box Superfamily:HMG-box Family:HMG-box 40 c3br8A_ not modelled 7.5 14 PDB header:hydrolase Chain: A: PDB Molecule:probable acylphosphatase; PDBTitle: crystal structure of acylphosphatase from bacillus subtilis 41 d2af7a1 not modelled 7.5 13 Fold:AhpD-like Superfamily:AhpD-like Family:CMD-like 42 d1j3da_ not modelled 7.4 16 Fold:HMG-box Superfamily:HMG-box Family:HMG-box 43 d1l3la1 not modelled 7.2 27 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) 44 c2lhjA_ not modelled 7.0 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:high mobility group protein homolog nhp1; PDBTitle: nmr structure of the high mobility group protein-like protein nhp12 from babesia bovis t2bo (baboa.00841.a) 45 c2xlkB_ not modelled 6.8 24 PDB header:hydrolase/rna Chain: B: PDB Molecule:csy4 endoribonuclease; PDBTitle: crystal structure of the csy4-crrna complex, orthorhombic form 46 c2gv1A_ not modelled 6.7 11 PDB header:hydrolase Chain: A: PDB Molecule:probable acylphosphatase; PDBTitle: nmr solution structure of the acylphosphatase from2 eschaerichia coli 47 c3qm2A_ not modelled 6.6 7 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 48 c2bjeA_ not modelled 6.5 19 PDB header:hydrolase Chain: A: PDB Molecule:acylphosphatase; PDBTitle: acylphosphatase from sulfolobus solfataricus. monclinic p212 space group 49 d1dwka2 not modelled 6.5 24 Fold:Cyanase C-terminal domain Superfamily:Cyanase C-terminal domain Family:Cyanase C-terminal domain 50 c2k1aA_ not modelled 6.4 10 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment 51 c2iv1J_ not modelled 6.3 16 PDB header:lyase Chain: J: PDB Molecule:cyanate hydratase; PDBTitle: site directed mutagenesis of key residues involved in the2 catalytic mechanism of cyanase 52 d1j5wa_ not modelled 6.1 25 Fold:Class II aaRS and biotin synthetases Superfamily:Class II aaRS and biotin synthetases Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain 53 d1jjcb4 not modelled 6.1 13 Fold:Ferredoxin-like Superfamily:Anticodon-binding domain of PheRS Family:Anticodon-binding domain of PheRS 54 c2crjA_ not modelled 6.0 24 PDB header:gene regulation Chain: A: PDB Molecule:swi/snf-related matrix-associated actin- PDBTitle: solution structure of the hmg domain of mouse hmg domain2 protein hmgx2 55 c2d88A_ not modelled 6.0 27 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 56 d1hsma_ not modelled 6.0 13 Fold:HMG-box Superfamily:HMG-box Family:HMG-box 57 c2d89A_ not modelled 5.6 23 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 58 d2lefa_ not modelled 5.5 19 Fold:HMG-box Superfamily:HMG-box Family:HMG-box 59 d2h3ja1 not modelled 5.4 13 Fold:SH3-like barrel Superfamily:C-terminal domain of transcriptional repressors Family:FeoA-like 60 c2kncB_ not modelled 5.3 19 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 61 c1wylA_ not modelled 5.1 24 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 62 c2e6oA_ not modelled 5.1 13 PDB header:transcription, cell cycle Chain: A: PDB Molecule:hmg box-containing protein 1; PDBTitle: solution structure of the hmg box domain from human hmg-box2 transcription factor 1

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