Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	F	G	H	I	A	Q	P	N	P	C	R	L	P	A	A	I	E	K	A	L	D	F	L	R	A	T	D	F	N	A	L	E	P	G	V	V	E	I	D	G	K	N	I	Y	T	Q	I	I	D	L	T	T	R	E	A	V	V	N
Secondary structure
SS confidence
Disorder		?	?	?	?																																																?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		R	P	E	V	H	R	R	Y	I	D	I	Q	F	L	A	W	G	E	E	K	I	G	I	A	I	D	T	G	N	N	K	V	S	E	S	L	L	E	Q	R	N	I	I	F	Y	H	D	S	E	H	E	S	F	I	E	M	I	P	G	S
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.
Sequence		Y	A	I	F	F	P	Q	D	V	H	R	P	G	C	I	M	Q	T	A	S	E	I	R	K	I	V	V	K	V	A	L	T	A	L	N
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 1s4c chain A domain 1 Region: 1 - 137 Aligned: 136 Modelled: 137 Confidence: 100.0% Identity: 30% Fold: Double-stranded beta-helix Superfamily: Clavaminate synthase-like Family: YhcH-like Phyre2 PDB 1yfu chain A domain 1 Region: 23 - 132 Aligned: 85 Modelled: 88 Confidence: 82.5% Identity: 12% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: 3-hydroxyanthranilic acid dioxygenase-like Phyre2 PDB 1v70 chain A Region: 41 - 150 Aligned: 80 Modelled: 84 Confidence: 70.9% Identity: 20% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: TM1287-like Phyre2 PDB 3cew chain A Region: 47 - 154 Aligned: 80 Modelled: 82 Confidence: 56.5% Identity: 20% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized cupin protein; PDBTitle: crystal structure of a cupin protein (bf4112) from bacteroides2 fragilis. northeast structural genomics consortium target bfr205 Phyre2 PDB 2i45 chain C Region: 61 - 132 Aligned: 47 Modelled: 47 Confidence: 47.5% Identity: 19% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of protein nmb1881 from neisseria meningitidis Phyre2 PDB 1o4t chain A Region: 46 - 149 Aligned: 76 Modelled: 78 Confidence: 42.0% Identity: 12% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: TM1287-like Phyre2 PDB 2xue chain B Region: 104 - 131 Aligned: 28 Modelled: 28 Confidence: 30.6% Identity: 18% PDB header:oxidoreductase Chain: B: PDB Molecule:lysine-specific demethylase 6b; PDBTitle: crystal structure of jmjd3 Phyre2 PDB 2xxz chain A Region: 112 - 131 Aligned: 20 Modelled: 20 Confidence: 29.2% Identity: 20% PDB header:oxidoreductase Chain: A: PDB Molecule:lysine-specific demethylase 6b; PDBTitle: crystal structure of the human jmjd3 jumonji domain Phyre2 PDB 2oa2 chain A Region: 47 - 124 Aligned: 77 Modelled: 78 Confidence: 27.4% Identity: 9% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:bh2720 protein; PDBTitle: crystal structure of bh2720 (10175341) from bacillus halodurans at2 1.41 a resolution Phyre2 PDB 1zvf chain A domain 1 Region: 23 - 132 Aligned: 88 Modelled: 92 Confidence: 25.3% Identity: 9% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: 3-hydroxyanthranilic acid dioxygenase-like Phyre2 PDB 2arc chain A Region: 112 - 139 Aligned: 28 Modelled: 28 Confidence: 23.8% Identity: 21% Fold: Double-stranded beta-helix Superfamily: Regulatory protein AraC Family: Regulatory protein AraC Phyre2 PDB 1vj2 chain A Region: 41 - 148 Aligned: 79 Modelled: 82 Confidence: 23.5% Identity: 15% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: TM1459-like Phyre2 PDB 3d82 chain A Region: 41 - 132 Aligned: 62 Modelled: 60 Confidence: 20.7% Identity: 16% PDB header:metal binding protein Chain: A: PDB Molecule:cupin 2, conserved barrel domain protein; PDBTitle: crystal structure of a cupin-2 domain containing protein (sfri_3543)2 from shewanella frigidimarina ncimb 400 at 2.05 a resolution Phyre2 PDB 2fqp chain D Region: 47 - 148 Aligned: 78 Modelled: 78 Confidence: 19.1% Identity: 10% PDB header:metal binding protein Chain: D: PDB Molecule:hypothetical protein bp2299; PDBTitle: crystal structure of a cupin domain (bp2299) from bordetella pertussis2 tohama i at 1.80 a resolution Phyre2 PDB 1a6q chain A domain 1 Region: 18 - 36 Aligned: 19 Modelled: 19 Confidence: 17.5% Identity: 21% Fold: Another 3-helical bundle Superfamily: Protein serine/threonine phosphatase 2C, C-terminal domain Family: Protein serine/threonine phosphatase 2C, C-terminal domain Phyre2 PDB 3ebr chain A Region: 116 - 147 Aligned: 32 Modelled: 32 Confidence: 15.9% Identity: 16% PDB header:unknown function Chain: A: PDB Molecule:uncharacterized rmlc-like cupin; PDBTitle: crystal structure of an rmlc-like cupin protein (reut_a0381) from2 ralstonia eutropha jmp134 at 2.60 a resolution Phyre2 PDB 2hdl chain A Region: 1 - 26 Aligned: 26 Modelled: 26 Confidence: 15.7% Identity: 12% PDB header:cytokine Chain: A: PDB Molecule:small inducible cytokine b14; PDBTitle: solution structure of brak/cxcl14 Phyre2 PDB 2pyh chain B Region: 16 - 42 Aligned: 27 Modelled: 27 Confidence: 15.4% Identity: 30% PDB header:isomerase Chain: B: PDB Molecule:poly(beta-d-mannuronate) c5 epimerase 4; PDBTitle: azotobacter vinelandii mannuronan c-5 epimerase alge4 a-module2 complexed with mannuronan trisaccharide Phyre2 PDB 2kku chain A Region: 78 - 147 Aligned: 64 Modelled: 70 Confidence: 15.0% Identity: 11% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of protein af2351 from archaeoglobus2 fulgidus. northeast structural genomics consortium target3 att9/ontario center for structural proteomics target af2351 Phyre2 PDB 2pa7 chain A domain 1 Region: 52 - 132 Aligned: 78 Modelled: 81 Confidence: 14.8% Identity: 12% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: dTDP-sugar isomerase Phyre2 1 d1s4ca1 2 d1yfua1 3 d1v70a_ 4 c3cewA_ 5 c2i45C_ 6 d1o4ta_ 7 c2xueB_ 8 c2xxzA_ 9 c2oa2A_ 10 d1zvfa1 11 d2arca_ 12 d1vj2a_ 13 c3d82A_ 14 c2fqpD_ 15 d1a6qa1 16 c3ebrA_ 17 c2hdlA_ 18 c2pyhB_ 19 c2kkuA_ 20 d2pa7a1 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

Detailed template information

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

1 d1s4ca1 100.0 30 Fold:Double-stranded beta-helix Superfamily:Clavaminate synthase-like Family:YhcH-like 2 d1yfua1 82.5 12 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:3-hydroxyanthranilic acid dioxygenase-like 3 d1v70a_ 70.9 20 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like 4 c3cewA_ 56.5 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized cupin protein; PDBTitle: crystal structure of a cupin protein (bf4112) from bacteroides2 fragilis. northeast structural genomics consortium target bfr205 5 c2i45C_ 47.5 19 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of protein nmb1881 from neisseria meningitidis 6 d1o4ta_ 42.0 12 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like 7 c2xueB_ 30.6 18 PDB header:oxidoreductase Chain: B: PDB Molecule:lysine-specific demethylase 6b; PDBTitle: crystal structure of jmjd3 8 c2xxzA_ 29.2 20 PDB header:oxidoreductase Chain: A: PDB Molecule:lysine-specific demethylase 6b; PDBTitle: crystal structure of the human jmjd3 jumonji domain 9 c2oa2A_ 27.4 9 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:bh2720 protein; PDBTitle: crystal structure of bh2720 (10175341) from bacillus halodurans at2 1.41 a resolution 10 d1zvfa1 25.3 9 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:3-hydroxyanthranilic acid dioxygenase-like 11 d2arca_ 23.8 21 Fold:Double-stranded beta-helix Superfamily:Regulatory protein AraC Family:Regulatory protein AraC 12 d1vj2a_ 23.5 15 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1459-like 13 c3d82A_ 20.7 16 PDB header:metal binding protein Chain: A: PDB Molecule:cupin 2, conserved barrel domain protein; PDBTitle: crystal structure of a cupin-2 domain containing protein (sfri_3543)2 from shewanella frigidimarina ncimb 400 at 2.05 a resolution 14 c2fqpD_ 19.1 10 PDB header:metal binding protein Chain: D: PDB Molecule:hypothetical protein bp2299; PDBTitle: crystal structure of a cupin domain (bp2299) from bordetella pertussis2 tohama i at 1.80 a resolution 15 d1a6qa1 17.5 21 Fold:Another 3-helical bundle Superfamily:Protein serine/threonine phosphatase 2C, C-terminal domain Family:Protein serine/threonine phosphatase 2C, C-terminal domain 16 c3ebrA_ 15.9 16 PDB header:unknown function Chain: A: PDB Molecule:uncharacterized rmlc-like cupin; PDBTitle: crystal structure of an rmlc-like cupin protein (reut_a0381) from2 ralstonia eutropha jmp134 at 2.60 a resolution 17 c2hdlA_ 15.7 12 PDB header:cytokine Chain: A: PDB Molecule:small inducible cytokine b14; PDBTitle: solution structure of brak/cxcl14 18 c2pyhB_ 15.4 30 PDB header:isomerase Chain: B: PDB Molecule:poly(beta-d-mannuronate) c5 epimerase 4; PDBTitle: azotobacter vinelandii mannuronan c-5 epimerase alge4 a-module2 complexed with mannuronan trisaccharide 19 c2kkuA_ 15.0 11 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of protein af2351 from archaeoglobus2 fulgidus. northeast structural genomics consortium target3 att9/ontario center for structural proteomics target af2351 20 d2pa7a1 14.8 12 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:dTDP-sugar isomerase 21 c3kgzA_ not modelled 14.3 16 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:cupin 2 conserved barrel domain protein; PDBTitle: crystal structure of a cupin 2 conserved barrel domain protein from2 rhodopseudomonas palustris 22 c2oziA_ not modelled 14.2 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein rpa4178; PDBTitle: structural genomics, the crystal structure of a putative2 protein rpa4178 from rhodopseudomonas palustris cga009 23 c2w2iC_ not modelled 13.8 20 PDB header:oxidoreductase Chain: C: PDB Molecule:2-oxoglutarate oxygenase; PDBTitle: crystal structure of the human 2-oxoglutarate oxygenase2 loc390245 24 d3dl3a1 not modelled 12.7 31 Fold:Double-stranded beta-helix Superfamily:Clavaminate synthase-like Family:TehB-like 25 c3bn8A_ not modelled 12.7 11 PDB header:transport protein Chain: A: PDB Molecule:putative sterol carrier protein 2; PDBTitle: crystal structure of a putative sterol carrier protein type 2 (af1534)2 from archaeoglobus fulgidus dsm 4304 at 2.11 a resolution 26 c2q8eB_ not modelled 12.2 25 PDB header:oxidoreductase Chain: B: PDB Molecule:jmjc domain-containing histone demethylation PDBTitle: specificity and mechanism of jmjd2a, a trimethyllysine-2 specific histone demethylase 27 c2os2A_ not modelled 12.1 25 PDB header:oxidoreductase Chain: A: PDB Molecule:jmjc domain-containing histone demethylation protein 3a; PDBTitle: crystal structure of jmjd2a complexed with histone h3 peptide2 trimethylated at lys36 28 d3bb6a1 not modelled 11.8 28 Fold:Double-stranded beta-helix Superfamily:Clavaminate synthase-like Family:TehB-like 29 d1y9qa2 not modelled 11.5 21 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Probable transcriptional regulator VC1968, C-terminal domain 30 d1j3pa_ not modelled 11.3 20 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Glucose-6-phosphate isomerase, GPI 31 d2es7a1 not modelled 11.3 29 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:HyaE-like 32 c2r32A_ not modelled 10.7 15 PDB header:immune system Chain: A: PDB Molecule:gcn4-pii/tumor necrosis factor ligand PDBTitle: crystal structure of human gitrl variant 33 c2ozjB_ not modelled 10.3 13 PDB header:unknown function Chain: B: PDB Molecule:cupin 2, conserved barrel; PDBTitle: crystal structure of a cupin superfamily protein (dsy2733) from2 desulfitobacterium hafniense dcb-2 at 1.60 a resolution 34 c2bx6A_ not modelled 10.2 12 PDB header:transduction protein Chain: A: PDB Molecule:xrp2 protein; PDBTitle: crystal structure of the human retinitis pigmentosa2 protein 2 (rp2) 35 c2yrvA_ not modelled 9.7 27 PDB header:transcription Chain: A: PDB Molecule:at-rich interactive domain-containing protein 4a; PDBTitle: solution structure of the rbb1nt domain of human2 rb(retinoblastoma)-binding protein 1 36 c2kpsA_ not modelled 9.0 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of domain iv from the ybbr family protein of2 desulfitobacterium hafniense 37 c3opwA_ not modelled 8.6 19 PDB header:oxidoreductase Chain: A: PDB Molecule:dna damage-responsive transcriptional repressor rph1; PDBTitle: crystal structure of the rph1 catalytic core 38 c2rq7A_ not modelled 8.1 16 PDB header:hydrolase Chain: A: PDB Molecule:atp synthase epsilon chain; PDBTitle: solution structure of the epsilon subunit chimera combining2 the n-terminal beta-sandwich domain from t. elongatus bp-13 f1 and the c-terminal alpha-helical domain from spinach4 chloroplast f1 39 d1xsqa_ not modelled 7.9 9 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Ureidoglycolate hydrolase AllA 40 c3fjsC_ not modelled 7.9 9 PDB header:biosynthetic protein Chain: C: PDB Molecule:uncharacterized protein with rmlc-like cupin fold; PDBTitle: crystal structure of a putative biosynthetic protein with rmlc-like2 cupin fold (reut_b4087) from ralstonia eutropha jmp134 at 1.90 a3 resolution 41 c2e5yA_ not modelled 7.9 19 PDB header:hydrolase Chain: A: PDB Molecule:atp synthase epsilon chain; PDBTitle: epsilon subunit and atp complex of f1f0-atp synthase from2 the thermophilic bacillus ps3 42 d1tvfa1 not modelled 7.7 19 Fold:Penicillin-binding protein associated domain Superfamily:Penicillin-binding protein associated domain Family:Pencillin binding protein 4 (PbpD), C-terminal domain 43 c3h8uA_ not modelled 7.6 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized conserved protein with double-stranded PDBTitle: crystal structure of uncharacterized conserved protein with double-2 stranded beta-helix domain (yp_001338853.1) from klebsiella3 pneumoniae subsp. pneumoniae mgh 78578 at 1.80 a resolution 44 c2zklA_ not modelled 7.5 9 PDB header:isomerase Chain: A: PDB Molecule:capsular polysaccharide synthesis enzyme cap5f; PDBTitle: crystal structure of capsular polysaccharide assembling protein capf2 from staphylococcus aureus 45 c3ibmB_ not modelled 7.2 9 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:cupin 2, conserved barrel domain protein; PDBTitle: crystal structure of cupin 2 domain-containing protein hhal_0468 from2 halorhodospira halophila 46 c2nnzA_ not modelled 7.2 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: solution structure of the hypothetical protein af2241 from2 archaeoglobus fulgidus 47 c3jurA_ not modelled 7.1 15 PDB header:hydrolase Chain: A: PDB Molecule:exo-poly-alpha-d-galacturonosidase; PDBTitle: the crystal structure of a hyperthermoactive exopolygalacturonase from2 thermotoga maritima 48 d1zx8a1 not modelled 7.0 15 Fold:Cyclophilin-like Superfamily:Cyclophilin-like Family:TM1367-like 49 d1lg4a_ not modelled 6.8 30 Fold:Prion-like Superfamily:Prion-like Family:Prion-like 50 c2qe7H_ not modelled 6.4 10 PDB header:hydrolase Chain: H: PDB Molecule:atp synthase subunit epsilon; PDBTitle: crystal structure of the f1-atpase from the thermoalkaliphilic2 bacterium bacillus sp. ta2.a1 51 c1fs0E_ not modelled 6.4 16 PDB header:hydrolase Chain: E: PDB Molecule:atp synthase epsilon subunit; PDBTitle: complex of gamma/epsilon atp synthase from e.coli 52 d1aqta2 not modelled 6.2 15 Fold:Epsilon subunit of F1F0-ATP synthase N-terminal domain Superfamily:Epsilon subunit of F1F0-ATP synthase N-terminal domain Family:Epsilon subunit of F1F0-ATP synthase N-terminal domain 53 c2ca9B_ not modelled 6.1 10 PDB header:transcriptional regulation Chain: B: PDB Molecule:putative nickel-responsive regulator; PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation 54 c2pfwB_ not modelled 6.1 15 PDB header:unknown function Chain: B: PDB Molecule:cupin 2, conserved barrel domain protein; PDBTitle: crystal structure of a rmlc-like cupin (sfri_3105) from shewanella2 frigidimarina ncimb 400 at 1.90 a resolution 55 c3tekA_ not modelled 5.8 10 PDB header:dna binding protein Chain: A: PDB Molecule:thermodbp-single stranded dna binding protein; PDBTitle: thermodbp: a non-canonical single-stranded dna binding protein with a2 novel structure and mechanism

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