Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	I	P	W	Q	D	L	S	P	E	T	L	E	N	L	I	E	S	F	V	L	R	E	G	T	D	Y	G	E	H	E	R	T	L	E	Q	K	V	A	D	V	K	R	Q	L	Q	C	G	E	A	V	L	V	W	S	E	L	H	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.
Sequence		T	V	N	I	M	P	R	S	Q	F	R	E
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 1y0n chain A Region: 1 - 70 Aligned: 62 Modelled: 70 Confidence: 100.0% Identity: 39% Fold: YehU-like Superfamily: YehU-like Family: YehU-like Phyre2 PDB 1g57 chain A Region: 37 - 68 Aligned: 31 Modelled: 32 Confidence: 83.2% Identity: 26% Fold: YrdC/RibB Superfamily: YrdC/RibB Family: 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB Phyre2 PDB 1snn chain A Region: 38 - 68 Aligned: 31 Modelled: 31 Confidence: 74.3% Identity: 26% Fold: YrdC/RibB Superfamily: YrdC/RibB Family: 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB Phyre2 PDB 1k4i chain A Region: 39 - 68 Aligned: 30 Modelled: 30 Confidence: 68.4% Identity: 27% Fold: YrdC/RibB Superfamily: YrdC/RibB Family: 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB Phyre2 PDB 3mio chain A Region: 39 - 68 Aligned: 30 Modelled: 30 Confidence: 59.6% Identity: 27% PDB header:lyase Chain: A: PDB Molecule:3,4-dihydroxy-2-butanone 4-phosphate synthase; PDBTitle: crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase2 domain from mycobacterium tuberculosis at ph 6.00 Phyre2 PDB 2nys chain A Region: 2 - 33 Aligned: 32 Modelled: 32 Confidence: 54.8% Identity: 25% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:agr_c_3712p; PDBTitle: x-ray crystal structure of protein agr_c_3712 from2 agrobacterium tumefaciens. northeast structural genomics3 consortium target atr88. Phyre2 PDB 2nys chain A domain 1 Region: 2 - 33 Aligned: 32 Modelled: 32 Confidence: 54.8% Identity: 25% Fold: SspB-like Superfamily: SspB-like Family: AGR C 3712p-like Phyre2 PDB 1tks chain A Region: 39 - 68 Aligned: 30 Modelled: 30 Confidence: 51.8% Identity: 23% Fold: YrdC/RibB Superfamily: YrdC/RibB Family: 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB Phyre2 PDB 2qas chain A Region: 2 - 33 Aligned: 32 Modelled: 31 Confidence: 43.1% Identity: 9% PDB header:hydrolase activator Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of caulobacter crescentus sspb ortholog Phyre2 PDB 2qaz chain C Region: 2 - 33 Aligned: 32 Modelled: 31 Confidence: 40.8% Identity: 9% PDB header:hydrolase activator Chain: C: PDB Molecule:sspb protein; PDBTitle: structure of c. crescentus sspb ortholog Phyre2 PDB 1k3e chain A Region: 3 - 23 Aligned: 21 Modelled: 21 Confidence: 35.4% Identity: 48% Fold: Secretion chaperone-like Superfamily: Type III secretory system chaperone-like Family: Type III secretory system chaperone Phyre2 PDB 3epu chain B Region: 3 - 21 Aligned: 19 Modelled: 19 Confidence: 30.0% Identity: 32% PDB header:chaperone Chain: B: PDB Molecule:stm2138 virulence chaperone; PDBTitle: crystal structure of stm2138, a novel virulence chaperone in2 salmonella Phyre2 PDB 2dal chain A Region: 9 - 27 Aligned: 19 Modelled: 19 Confidence: 19.3% Identity: 26% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein kiaa0794; PDBTitle: solution structure of the novel identified uba-like domain2 in the n-terminal of human fas associated factor 1 protein Phyre2 PDB 1ux8 chain A Region: 4 - 23 Aligned: 20 Modelled: 20 Confidence: 19.1% Identity: 30% Fold: Globin-like Superfamily: Globin-like Family: Truncated hemoglobin Phyre2 PDB 2yr1 chain B Region: 5 - 56 Aligned: 52 Modelled: 52 Confidence: 18.0% Identity: 25% PDB header:lyase Chain: B: PDB Molecule:3-dehydroquinate dehydratase; PDBTitle: crystal structure of 3-dehydroquinate dehydratase from geobacillus2 kaustophilus hta426 Phyre2 PDB 2csb chain A domain 1 Region: 8 - 20 Aligned: 13 Modelled: 13 Confidence: 17.3% Identity: 54% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: Topoisomerase V repeat domain Phyre2 PDB 1f7u chain A domain 3 Region: 8 - 29 Aligned: 22 Modelled: 22 Confidence: 17.0% Identity: 32% Fold: RRF/tRNA synthetase additional domain-like Superfamily: Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain Family: Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain Phyre2 PDB 2ig3 chain A Region: 4 - 23 Aligned: 20 Modelled: 20 Confidence: 17.0% Identity: 20% PDB header:oxygen storage/transport Chain: A: PDB Molecule:group iii truncated haemoglobin; PDBTitle: crystal structure of group iii truncated hemoglobin from campylobacter2 jejuni Phyre2 PDB 1vyu chain B Region: 20 - 71 Aligned: 52 Modelled: 52 Confidence: 13.4% Identity: 8% PDB header:ion transport Chain: B: PDB Molecule:calcium channel beta-3 subunit; PDBTitle: beta3 subunit of voltage-gated ca2+-channel Phyre2 PDB 3nrt chain C Region: 1 - 11 Aligned: 11 Modelled: 11 Confidence: 12.2% Identity: 36% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:putative ryanodine receptor; PDBTitle: the crystal strucutre of putative ryanodine receptor from bacteroides2 thetaiotaomicron vpi-5482 Phyre2 1 d1y0na_ 2 d1g57a_ 3 d1snna_ 4 d1k4ia_ 5 c3mioA_ 6 c2nysA_ 7 d2nysa1 8 d1tksa_ 9 c2qasA_ 10 c2qazC_ 11 d1k3ea_ 12 c3epuB_ 13 c2dalA_ 14 d1ux8a_ 15 c2yr1B_ 16 d2csba1 17 d1f7ua3 18 c2ig3A_ 19 c1vyuB_ 20 c3nrtC_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43

Detailed template information

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

1 d1y0na_ 100.0 39 Fold:YehU-like Superfamily:YehU-like Family:YehU-like 2 d1g57a_ 83.2 26 Fold:YrdC/RibB Superfamily:YrdC/RibB Family:3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB 3 d1snna_ 74.3 26 Fold:YrdC/RibB Superfamily:YrdC/RibB Family:3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB 4 d1k4ia_ 68.4 27 Fold:YrdC/RibB Superfamily:YrdC/RibB Family:3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB 5 c3mioA_ 59.6 27 PDB header:lyase Chain: A: PDB Molecule:3,4-dihydroxy-2-butanone 4-phosphate synthase; PDBTitle: crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase2 domain from mycobacterium tuberculosis at ph 6.00 6 c2nysA_ 54.8 25 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:agr_c_3712p; PDBTitle: x-ray crystal structure of protein agr_c_3712 from2 agrobacterium tumefaciens. northeast structural genomics3 consortium target atr88. 7 d2nysa1 54.8 25 Fold:SspB-like Superfamily:SspB-like Family:AGR C 3712p-like 8 d1tksa_ 51.8 23 Fold:YrdC/RibB Superfamily:YrdC/RibB Family:3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB 9 c2qasA_ 43.1 9 PDB header:hydrolase activator Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of caulobacter crescentus sspb ortholog 10 c2qazC_ 40.8 9 PDB header:hydrolase activator Chain: C: PDB Molecule:sspb protein; PDBTitle: structure of c. crescentus sspb ortholog 11 d1k3ea_ 35.4 48 Fold:Secretion chaperone-like Superfamily:Type III secretory system chaperone-like Family:Type III secretory system chaperone 12 c3epuB_ 30.0 32 PDB header:chaperone Chain: B: PDB Molecule:stm2138 virulence chaperone; PDBTitle: crystal structure of stm2138, a novel virulence chaperone in2 salmonella 13 c2dalA_ 19.3 26 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein kiaa0794; PDBTitle: solution structure of the novel identified uba-like domain2 in the n-terminal of human fas associated factor 1 protein 14 d1ux8a_ 19.1 30 Fold:Globin-like Superfamily:Globin-like Family:Truncated hemoglobin 15 c2yr1B_ 18.0 25 PDB header:lyase Chain: B: PDB Molecule:3-dehydroquinate dehydratase; PDBTitle: crystal structure of 3-dehydroquinate dehydratase from geobacillus2 kaustophilus hta426 16 d2csba1 17.3 54 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Topoisomerase V repeat domain 17 d1f7ua3 17.0 32 Fold:RRF/tRNA synthetase additional domain-like Superfamily:Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain Family:Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain 18 c2ig3A_ 17.0 20 PDB header:oxygen storage/transport Chain: A: PDB Molecule:group iii truncated haemoglobin; PDBTitle: crystal structure of group iii truncated hemoglobin from campylobacter2 jejuni 19 c1vyuB_ 13.4 8 PDB header:ion transport Chain: B: PDB Molecule:calcium channel beta-3 subunit; PDBTitle: beta3 subunit of voltage-gated ca2+-channel 20 c3nrtC_ 12.2 36 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:putative ryanodine receptor; PDBTitle: the crystal strucutre of putative ryanodine receptor from bacteroides2 thetaiotaomicron vpi-5482 21 d2c1ia1 not modelled 11.4 20 Fold:7-stranded beta/alpha barrel Superfamily:Glycoside hydrolase/deacetylase Family:NodB-like polysaccharide deacetylase 22 c3rqrA_ not modelled 10.9 25 PDB header:metal transport Chain: A: PDB Molecule:ryanodine receptor 1; PDBTitle: crystal structure of the ryr domain of the rabbit ryanodine receptor 23 c2l57A_ not modelled 10.6 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of an uncharacterized thioredoin-like protein from2 clostridium perfringens 24 d1iaza_ not modelled 10.4 28 Fold:Cytolysin/lectin Superfamily:Cytolysin/lectin Family:Anemone pore-forming cytolysin 25 d1ttwa_ not modelled 9.4 26 Fold:Secretion chaperone-like Superfamily:Type III secretory system chaperone-like Family:Type III secretory system chaperone 26 d1f1sa3 not modelled 9.1 6 Fold:Hyaluronate lyase-like, C-terminal domain Superfamily:Hyaluronate lyase-like, C-terminal domain Family:Hyaluronate lyase-like, C-terminal domain 27 d1gwya_ not modelled 9.1 22 Fold:Cytolysin/lectin Superfamily:Cytolysin/lectin Family:Anemone pore-forming cytolysin 28 c3rhtB_ not modelled 8.0 19 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:(gatase1)-like protein; PDBTitle: crystal structure of type 1 glutamine amidotransferase (gatase1)-like2 protein from planctomyces limnophilus 29 d1t1ha_ not modelled 7.9 25 Fold:RING/U-box Superfamily:RING/U-box Family:U-box 30 c2kkmA_ not modelled 7.9 25 PDB header:translation Chain: A: PDB Molecule:translation machinery-associated protein 16; PDBTitle: solution nmr structure of yeast protein yor252w [residues2 38-178]: northeast structural genomics consortium target3 yt654 31 d1n7oa2 not modelled 7.8 11 Fold:Hyaluronate lyase-like, C-terminal domain Superfamily:Hyaluronate lyase-like, C-terminal domain Family:Hyaluronate lyase-like, C-terminal domain 32 d1zata2 not modelled 7.6 13 Fold:L,D-transpeptidase pre-catalytic domain-like Superfamily:L,D-transpeptidase pre-catalytic domain-like Family:L,D-transpeptidase pre-catalytic domain-like 33 c3o85A_ not modelled 6.7 29 PDB header:ribosomal protein Chain: A: PDB Molecule:ribosomal protein l7ae; PDBTitle: giardia lamblia 15.5kd rna binding protein 34 c3pkzK_ not modelled 6.7 16 PDB header:recombination Chain: K: PDB Molecule:recombinase sin; PDBTitle: structural basis for catalytic activation of a serine recombinase 35 d1d8wa_ not modelled 6.4 25 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:L-rhamnose isomerase 36 d1wmha_ not modelled 6.2 16 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 37 d1j75a_ not modelled 5.9 45 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Z-DNA binding domain 38 d1ixrc1 not modelled 5.6 39 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Helicase DNA-binding domain 39 d1ueab_ not modelled 5.4 25 Fold:OB-fold Superfamily:TIMP-like Family:Tissue inhibitor of metalloproteinases, TIMP 40 d2ozba1 not modelled 5.4 12 Fold:Bacillus chorismate mutase-like Superfamily:L30e-like Family:L30e/L7ae ribosomal proteins 41 c3uowB_ not modelled 5.3 10 PDB header:ligase Chain: B: PDB Molecule:gmp synthetase; PDBTitle: crystal structure of pf10_0123, a gmp synthetase from plasmodium2 falciparum 42 c2cb1A_ not modelled 5.3 20 PDB header:lyase Chain: A: PDB Molecule:o-acetyl homoserine sulfhydrylase; PDBTitle: crystal structure of o-actetyl homoserine sulfhydrylase2 from thermus thermophilus hb8,oah2. 43 c1fqvK_ not modelled 5.2 25 PDB header:ligase Chain: K: PDB Molecule:skp2; PDBTitle: insights into scf ubiquitin ligases from the structure of2 the skp1-skp2 complex

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