Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	I	I	D	N	L	E	Q	F	R	Q	I	Y	A	S	G	K	K	W	Q	R	C	V	E	A	I	E	N	I	D	N	I	Q	P	G	V	A	H	S	I	G	D	S	L	T	Y	R	V	E	T	D	S	A	T	D	A	L	F	T
Secondary structure
SS confidence
Disorder		?				?																														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	H	R	R	Y	F	E	V	H	Y	Y	L	Q	G	Q	Q	K	I	E	Y	A	P	K	E	T	L	Q	V	V	E	Y	Y	R	D	E	T	D	R	E	Y	L	K	G	C	G	E	T	V	E	V	H	E	G	Q	I	V	I	C	D	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.
Sequence		H	E	A	Y	R	F	I	C	N	N	A	V	K	K	V	V	L	K	V	T	I	E	D	G	Y	F	H	N	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 1s4c chain A domain 1 Region: 2 - 132 Aligned: 130 Modelled: 131 Confidence: 100.0% Identity: 18% Fold: Double-stranded beta-helix Superfamily: Clavaminate synthase-like Family: YhcH-like Phyre2 PDB 1yfu chain A domain 1 Region: 25 - 126 Aligned: 82 Modelled: 83 Confidence: 90.4% Identity: 17% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: 3-hydroxyanthranilic acid dioxygenase-like Phyre2 PDB 2i45 chain C Region: 59 - 137 Aligned: 57 Modelled: 57 Confidence: 83.1% Identity: 16% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of protein nmb1881 from neisseria meningitidis Phyre2 PDB 3cew chain A Region: 42 - 145 Aligned: 81 Modelled: 81 Confidence: 75.8% Identity: 14% 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 2arc chain A Region: 58 - 125 Aligned: 44 Modelled: 45 Confidence: 70.5% Identity: 23% Fold: Double-stranded beta-helix Superfamily: Regulatory protein AraC Family: Regulatory protein AraC Phyre2 PDB 2pa7 chain A domain 1 Region: 43 - 126 Aligned: 82 Modelled: 84 Confidence: 58.2% Identity: 13% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: dTDP-sugar isomerase Phyre2 PDB 3d82 chain A Region: 59 - 137 Aligned: 56 Modelled: 55 Confidence: 52.5% 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 1v70 chain A Region: 40 - 140 Aligned: 78 Modelled: 78 Confidence: 46.2% Identity: 14% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: TM1287-like Phyre2 PDB 1o4t chain A Region: 45 - 139 Aligned: 72 Modelled: 72 Confidence: 46.0% Identity: 22% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: TM1287-like Phyre2 PDB 2opk chain C Region: 70 - 125 Aligned: 35 Modelled: 34 Confidence: 32.8% Identity: 20% PDB header:isomerase Chain: C: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a putative mannose-6-phosphate isomerase2 (reut_a1446) from ralstonia eutropha jmp134 at 2.10 a resolution Phyre2 PDB 2ozj chain B Region: 40 - 140 Aligned: 78 Modelled: 78 Confidence: 30.0% Identity: 12% 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 Phyre2 PDB 2oa2 chain A Region: 41 - 140 Aligned: 83 Modelled: 83 Confidence: 29.2% Identity: 13% 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 1j0s chain A Region: 70 - 138 Aligned: 60 Modelled: 69 Confidence: 25.5% Identity: 23% Fold: beta-Trefoil Superfamily: Cytokine Family: Interleukin-1 (IL-1) Phyre2 PDB 3ht2 chain A Region: 42 - 147 Aligned: 85 Modelled: 85 Confidence: 24.9% Identity: 16% PDB header:lyase Chain: A: PDB Molecule:remf protein; PDBTitle: zink containing polyketide cyclase remf from streptomyces2 resistomycificus Phyre2 PDB 2o8q chain A Region: 59 - 140 Aligned: 60 Modelled: 60 Confidence: 24.0% Identity: 22% PDB header:metal binding protein Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a protein with a cupin-like fold and unknown2 function (bxe_c0505) from burkholderia xenovorans lb400 at 1.55 a3 resolution Phyre2 PDB 2xp1 chain A Region: 111 - 149 Aligned: 30 Modelled: 38 Confidence: 21.9% Identity: 13% PDB header:transcription Chain: A: PDB Molecule:spt6; PDBTitle: structure of the tandem sh2 domains from antonospora locustae2 transcription elongation factor spt6 Phyre2 PDB 1lr5 chain A Region: 43 - 137 Aligned: 81 Modelled: 81 Confidence: 21.9% Identity: 9% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: Germin/Seed storage 7S protein Phyre2 PDB 3bcw chain B Region: 59 - 141 Aligned: 61 Modelled: 61 Confidence: 21.4% Identity: 21% PDB header:unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a duf861 family protein with a rmlc-like cupin2 fold (bb1179) from bordetella bronchiseptica rb50 at 1.60 a3 resolution Phyre2 PDB 2xxz chain A Region: 104 - 125 Aligned: 22 Modelled: 22 Confidence: 21.1% Identity: 9% PDB header:oxidoreductase Chain: A: PDB Molecule:lysine-specific demethylase 6b; PDBTitle: crystal structure of the human jmjd3 jumonji domain Phyre2 PDB 1zvf chain A domain 1 Region: 25 - 137 Aligned: 97 Modelled: 98 Confidence: 20.7% Identity: 7% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: 3-hydroxyanthranilic acid dioxygenase-like Phyre2 1 d1s4ca1 2 d1yfua1 3 c2i45C_ 4 c3cewA_ 5 d2arca_ 6 d2pa7a1 7 c3d82A_ 8 d1v70a_ 9 d1o4ta_ 10 c2opkC_ 11 c2ozjB_ 12 c2oa2A_ 13 d1j0sa_ 14 c3ht2A_ 15 c2o8qA_ 16 c2xp1A_ 17 d1lr5a_ 18 c3bcwB_ 19 c2xxzA_ 20 d1zvfa1 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

Detailed template information

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

1 d1s4ca1 100.0 18 Fold:Double-stranded beta-helix Superfamily:Clavaminate synthase-like Family:YhcH-like 2 d1yfua1 90.4 17 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:3-hydroxyanthranilic acid dioxygenase-like 3 c2i45C_ 83.1 16 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of protein nmb1881 from neisseria meningitidis 4 c3cewA_ 75.8 14 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 d2arca_ 70.5 23 Fold:Double-stranded beta-helix Superfamily:Regulatory protein AraC Family:Regulatory protein AraC 6 d2pa7a1 58.2 13 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:dTDP-sugar isomerase 7 c3d82A_ 52.5 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 8 d1v70a_ 46.2 14 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like 9 d1o4ta_ 46.0 22 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like 10 c2opkC_ 32.8 20 PDB header:isomerase Chain: C: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a putative mannose-6-phosphate isomerase2 (reut_a1446) from ralstonia eutropha jmp134 at 2.10 a resolution 11 c2ozjB_ 30.0 12 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 12 c2oa2A_ 29.2 13 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 13 d1j0sa_ 25.5 23 Fold:beta-Trefoil Superfamily:Cytokine Family:Interleukin-1 (IL-1) 14 c3ht2A_ 24.9 16 PDB header:lyase Chain: A: PDB Molecule:remf protein; PDBTitle: zink containing polyketide cyclase remf from streptomyces2 resistomycificus 15 c2o8qA_ 24.0 22 PDB header:metal binding protein Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a protein with a cupin-like fold and unknown2 function (bxe_c0505) from burkholderia xenovorans lb400 at 1.55 a3 resolution 16 c2xp1A_ 21.9 13 PDB header:transcription Chain: A: PDB Molecule:spt6; PDBTitle: structure of the tandem sh2 domains from antonospora locustae2 transcription elongation factor spt6 17 d1lr5a_ 21.9 9 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 18 c3bcwB_ 21.4 21 PDB header:unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a duf861 family protein with a rmlc-like cupin2 fold (bb1179) from bordetella bronchiseptica rb50 at 1.60 a3 resolution 19 c2xxzA_ 21.1 9 PDB header:oxidoreductase Chain: A: PDB Molecule:lysine-specific demethylase 6b; PDBTitle: crystal structure of the human jmjd3 jumonji domain 20 d1zvfa1 20.7 7 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:3-hydroxyanthranilic acid dioxygenase-like 21 c2q30C_ not modelled 20.5 13 PDB header:unknown function Chain: C: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a rmlc-like cupin protein (dde_2303) from2 desulfovibrio desulfuricans subsp. at 1.94 a resolution 22 d1vj2a_ not modelled 20.1 18 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1459-like 23 d1x82a_ not modelled 17.1 28 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Glucose-6-phosphate isomerase, GPI 24 c3kgzA_ not modelled 16.8 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 25 c2xueB_ not modelled 15.1 11 PDB header:oxidoreductase Chain: B: PDB Molecule:lysine-specific demethylase 6b; PDBTitle: crystal structure of jmjd3 26 c2pfwB_ not modelled 14.9 13 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 27 d1j3pa_ not modelled 13.7 22 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Glucose-6-phosphate isomerase, GPI 28 d3dl3a1 not modelled 12.7 13 Fold:Double-stranded beta-helix Superfamily:Clavaminate synthase-like Family:TehB-like 29 d1o5ua_ not modelled 11.7 25 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Hypothetical protein TM1112 30 d3bb6a1 not modelled 11.3 8 Fold:Double-stranded beta-helix Superfamily:Clavaminate synthase-like Family:TehB-like 31 d1yhfa1 not modelled 10.8 21 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like 32 c3fjsC_ not modelled 10.8 18 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 33 c3l2hD_ not modelled 10.5 26 PDB header:isomerase Chain: D: PDB Molecule:putative sugar phosphate isomerase; PDBTitle: crystal structure of putative sugar phosphate isomerase (afe_0303)2 from acidithiobacillus ferrooxidans atcc 23270 at 1.85 a resolution 34 c2vqaC_ not modelled 10.0 15 PDB header:metal-binding protein Chain: C: PDB Molecule:sll1358 protein; PDBTitle: protein-folding location can regulate mn versus cu- or zn-2 binding. crystal structure of mnca. 35 c3ibmB_ not modelled 9.8 16 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 36 c3ebrA_ not modelled 9.2 18 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 37 c3jzvA_ not modelled 7.5 16 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein rru_a2000; PDBTitle: crystal structure of rru_a2000 from rhodospirillum rubrum: a cupin-22 domain. 38 c2w2iC_ not modelled 7.2 5 PDB header:oxidoreductase Chain: C: PDB Molecule:2-oxoglutarate oxygenase; PDBTitle: crystal structure of the human 2-oxoglutarate oxygenase2 loc390245 39 d1dgwa_ not modelled 7.1 14 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 40 c2odbB_ not modelled 6.7 13 PDB header:protein binding Chain: B: PDB Molecule:serine/threonine-protein kinase pak 6; PDBTitle: the crystal structure of human cdc42 in complex with the crib domain2 of human p21-activated kinase 6 (pak6) 41 c2ca9B_ not modelled 6.3 9 PDB header:transcriptional regulation Chain: B: PDB Molecule:putative nickel-responsive regulator; PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation 42 c2os2A_ not modelled 6.1 14 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 43 c2q8eB_ not modelled 6.1 14 PDB header:oxidoreductase Chain: B: PDB Molecule:jmjc domain-containing histone demethylation PDBTitle: specificity and mechanism of jmjd2a, a trimethyllysine-2 specific histone demethylase 44 d1y9qa2 not modelled 5.8 12 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Probable transcriptional regulator VC1968, C-terminal domain 45 c3opwA_ not modelled 5.8 19 PDB header:oxidoreductase Chain: A: PDB Molecule:dna damage-responsive transcriptional repressor rph1; PDBTitle: crystal structure of the rph1 catalytic core 46 d1sfna_ not modelled 5.7 19 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:YlbA-like 47 d1rc6a_ not modelled 5.6 20 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:YlbA-like 48 d2es7a1 not modelled 5.4 29 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:HyaE-like

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