Secondary structure and disorder prediction

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Sequence		M	L	I	L	T	R	R	V	G	E	T	L	M	I	G	D	E	V	T	V	T	V	L	G	V	K	G	N	Q	V	R	I	G	V	N	A	P	K	E	V	S	V	H	R	E	E	I	Y	Q	R	I	Q	A	E	K	S	Q	Q	S	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?																																																					?	?	?
Disorder confidence
		.
Sequence		Y
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 1t3o chain A Region: 1 - 61 Aligned: 61 Modelled: 61 Confidence: 99.9% Identity: 41% PDB header:rna binding protein Chain: A: PDB Molecule:carbon storage regulator; PDBTitle: solution structure of csra, a bacterial carbon storage2 regulatory protein Phyre2 PDB 2jpp chain B Region: 1 - 53 Aligned: 53 Modelled: 53 Confidence: 99.9% Identity: 75% PDB header:translation/rna Chain: B: PDB Molecule:translational repressor; PDBTitle: structural basis of rsma/csra rna recognition: structure of2 rsme bound to the shine-dalgarno sequence of hcna mrna Phyre2 PDB 1vpz chain A Region: 1 - 54 Aligned: 54 Modelled: 53 Confidence: 99.9% Identity: 89% Fold: CsrA-like Superfamily: CsrA-like Family: CsrA-like Phyre2 PDB 1vpz chain B Region: 1 - 53 Aligned: 53 Modelled: 52 Confidence: 99.9% Identity: 89% PDB header:rna binding protein Chain: B: PDB Molecule:carbon storage regulator homolog; PDBTitle: crystal structure of a putative carbon storage regulator protein2 (csra, pa0905) from pseudomonas aeruginosa at 2.05 a resolution Phyre2 PDB 1e0t chain A domain 1 Region: 7 - 32 Aligned: 26 Modelled: 26 Confidence: 63.3% Identity: 31% Fold: PK beta-barrel domain-like Superfamily: PK beta-barrel domain-like Family: Pyruvate kinase beta-barrel domain Phyre2 PDB 2g50 chain A domain 1 Region: 7 - 35 Aligned: 29 Modelled: 29 Confidence: 62.7% Identity: 17% Fold: PK beta-barrel domain-like Superfamily: PK beta-barrel domain-like Family: Pyruvate kinase beta-barrel domain Phyre2 PDB 1pkm chain A domain 1 Region: 7 - 34 Aligned: 28 Modelled: 28 Confidence: 60.6% Identity: 18% Fold: PK beta-barrel domain-like Superfamily: PK beta-barrel domain-like Family: Pyruvate kinase beta-barrel domain Phyre2 PDB 1liu chain A domain 1 Region: 7 - 35 Aligned: 29 Modelled: 29 Confidence: 59.6% Identity: 21% Fold: PK beta-barrel domain-like Superfamily: PK beta-barrel domain-like Family: Pyruvate kinase beta-barrel domain Phyre2 PDB 1e0t chain D Region: 7 - 31 Aligned: 25 Modelled: 25 Confidence: 38.5% Identity: 32% PDB header:phosphotransferase Chain: D: PDB Molecule:pyruvate kinase; PDBTitle: r292d mutant of e. coli pyruvate kinase Phyre2 PDB 2o3g chain A domain 1 Region: 7 - 31 Aligned: 24 Modelled: 25 Confidence: 35.6% Identity: 17% Fold: FAD-binding/transporter-associated domain-like Superfamily: FAD-binding/transporter-associated domain-like Family: CorC/HlyC domain-like Phyre2 PDB 3eoe chain C Region: 7 - 31 Aligned: 25 Modelled: 25 Confidence: 34.2% Identity: 32% PDB header:transferase Chain: C: PDB Molecule:pyruvate kinase; PDBTitle: crystal structure of pyruvate kinase from toxoplasma gondii, 55.m00007 Phyre2 PDB 1vhk chain A domain 1 Region: 3 - 34 Aligned: 32 Modelled: 32 Confidence: 34.0% Identity: 19% Fold: PUA domain-like Superfamily: PUA domain-like Family: YggJ N-terminal domain-like Phyre2 PDB 3ila chain G Region: 6 - 21 Aligned: 16 Modelled: 16 Confidence: 31.3% Identity: 31% PDB header:signaling protein Chain: G: PDB Molecule:ryanodine receptor 1; PDBTitle: crystal structure of rabbit ryanodine receptor 1 n-terminal domain (9-2 205) Phyre2 PDB 1t5a chain B Region: 7 - 31 Aligned: 25 Modelled: 25 Confidence: 30.6% Identity: 16% PDB header:transferase Chain: B: PDB Molecule:pyruvate kinase, m2 isozyme; PDBTitle: human pyruvate kinase m2 Phyre2 PDB 2o1r chain A domain 1 Region: 7 - 31 Aligned: 24 Modelled: 25 Confidence: 30.3% Identity: 29% Fold: FAD-binding/transporter-associated domain-like Superfamily: FAD-binding/transporter-associated domain-like Family: CorC/HlyC domain-like Phyre2 PDB 1aqf chain B Region: 7 - 31 Aligned: 25 Modelled: 25 Confidence: 29.3% Identity: 16% PDB header:transferase Chain: B: PDB Molecule:pyruvate kinase; PDBTitle: pyruvate kinase from rabbit muscle with mg, k, and l-2 phospholactate Phyre2 PDB 1a3x chain A domain 1 Region: 7 - 28 Aligned: 22 Modelled: 22 Confidence: 28.7% Identity: 23% Fold: PK beta-barrel domain-like Superfamily: PK beta-barrel domain-like Family: Pyruvate kinase beta-barrel domain Phyre2 PDB 1go3 chain E Region: 5 - 37 Aligned: 33 Modelled: 33 Confidence: 28.2% Identity: 24% PDB header:transferase Chain: E: PDB Molecule:dna-directed rna polymerase subunit e; PDBTitle: structure of an archeal homolog of the eukaryotic rna2 polymerase ii rpb4/rpb7 complex Phyre2 PDB 1pkl chain A domain 1 Region: 7 - 30 Aligned: 24 Modelled: 24 Confidence: 27.8% Identity: 25% Fold: PK beta-barrel domain-like Superfamily: PK beta-barrel domain-like Family: Pyruvate kinase beta-barrel domain Phyre2 PDB 1pmi chain A Region: 1 - 42 Aligned: 41 Modelled: 42 Confidence: 27.3% Identity: 22% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: Type I phosphomannose isomerase Phyre2 1 c1t3oA_ 2 c2jppB_ 3 d1vpza_ 4 c1vpzB_ 5 d1e0ta1 6 d2g50a1 7 d1pkma1 8 d1liua1 9 c1e0tD_ 10 d2o3ga1 11 c3eoeC_ 12 d1vhka1 13 c3ilaG_ 14 c1t5aB_ 15 d2o1ra1 16 c1aqfB_ 17 d1a3xa1 18 c1go3E_ 19 d1pkla1 20 d1pmia_ 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 73 74 75

Detailed template information

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

1 c1t3oA_ 99.9 41 PDB header:rna binding protein Chain: A: PDB Molecule:carbon storage regulator; PDBTitle: solution structure of csra, a bacterial carbon storage2 regulatory protein 2 c2jppB_ 99.9 75 PDB header:translation/rna Chain: B: PDB Molecule:translational repressor; PDBTitle: structural basis of rsma/csra rna recognition: structure of2 rsme bound to the shine-dalgarno sequence of hcna mrna 3 d1vpza_ 99.9 89 Fold:CsrA-like Superfamily:CsrA-like Family:CsrA-like 4 c1vpzB_ 99.9 89 PDB header:rna binding protein Chain: B: PDB Molecule:carbon storage regulator homolog; PDBTitle: crystal structure of a putative carbon storage regulator protein2 (csra, pa0905) from pseudomonas aeruginosa at 2.05 a resolution 5 d1e0ta1 63.3 31 Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain 6 d2g50a1 62.7 17 Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain 7 d1pkma1 60.6 18 Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain 8 d1liua1 59.6 21 Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain 9 c1e0tD_ 38.5 32 PDB header:phosphotransferase Chain: D: PDB Molecule:pyruvate kinase; PDBTitle: r292d mutant of e. coli pyruvate kinase 10 d2o3ga1 35.6 17 Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like 11 c3eoeC_ 34.2 32 PDB header:transferase Chain: C: PDB Molecule:pyruvate kinase; PDBTitle: crystal structure of pyruvate kinase from toxoplasma gondii, 55.m00007 12 d1vhka1 34.0 19 Fold:PUA domain-like Superfamily:PUA domain-like Family:YggJ N-terminal domain-like 13 c3ilaG_ 31.3 31 PDB header:signaling protein Chain: G: PDB Molecule:ryanodine receptor 1; PDBTitle: crystal structure of rabbit ryanodine receptor 1 n-terminal domain (9-2 205) 14 c1t5aB_ 30.6 16 PDB header:transferase Chain: B: PDB Molecule:pyruvate kinase, m2 isozyme; PDBTitle: human pyruvate kinase m2 15 d2o1ra1 30.3 29 Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like 16 c1aqfB_ 29.3 16 PDB header:transferase Chain: B: PDB Molecule:pyruvate kinase; PDBTitle: pyruvate kinase from rabbit muscle with mg, k, and l-2 phospholactate 17 d1a3xa1 28.7 23 Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain 18 c1go3E_ 28.2 24 PDB header:transferase Chain: E: PDB Molecule:dna-directed rna polymerase subunit e; PDBTitle: structure of an archeal homolog of the eukaryotic rna2 polymerase ii rpb4/rpb7 complex 19 d1pkla1 27.8 25 Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain 20 d1pmia_ 27.3 22 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Type I phosphomannose isomerase 21 c2eqsA_ not modelled 26.2 26 PDB header:hydrolase Chain: A: PDB Molecule:atp-dependent rna helicase dhx8; PDBTitle: solution structure of the s1 rna binding domain of human2 atp-dependent rna helicase dhx8 22 c3llbA_ not modelled 22.8 25 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: the crystal structure of the protein pa3983 with unknown2 function from pseudomonas aeruginosa pao1 23 c3ma8A_ not modelled 21.1 24 PDB header:transferase Chain: A: PDB Molecule:pyruvate kinase; PDBTitle: crystal structure of cgd1_2040, a pyruvate kinase from cryptosporidium2 parvum 24 d2r2za1 not modelled 20.0 16 Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like 25 c3ec1A_ not modelled 19.6 24 PDB header:hydrolase, signaling protein Chain: A: PDB Molecule:yqeh gtpase; PDBTitle: structure of yqeh gtpase from geobacillus stearothermophilus2 (an atnos1 / atnoa1 ortholog) 26 c3dedB_ not modelled 19.6 13 PDB header:membrane protein Chain: B: PDB Molecule:probable hemolysin; PDBTitle: c-terminal domain of probable hemolysin from chromobacterium violaceum 27 c3h0gS_ not modelled 18.3 16 PDB header:transcription Chain: S: PDB Molecule:dna-directed rna polymerase ii subunit rpb7; PDBTitle: rna polymerase ii from schizosaccharomyces pombe 28 d2z0sa1 not modelled 18.2 18 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 29 c2xrhA_ not modelled 16.5 29 PDB header:unknown function Chain: A: PDB Molecule:protein hp0721; PDBTitle: crystal structure of the truncated form of hp0721 30 d3deda1 not modelled 15.7 13 Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like 31 c2khiA_ not modelled 14.8 24 PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s1; PDBTitle: nmr structure of the domain 4 of the e. coli ribosomal2 protein s1 32 c1pklB_ not modelled 14.6 25 PDB header:transferase Chain: B: PDB Molecule:protein (pyruvate kinase); PDBTitle: the structure of leishmania pyruvate kinase 33 d1y14b1 not modelled 14.4 13 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 34 d2p13a1 not modelled 13.7 17 Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like 35 d2nqwa1 not modelled 13.2 17 Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like 36 c2khjA_ not modelled 12.9 32 PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s1; PDBTitle: nmr structure of the domain 6 of the e. coli ribosomal2 protein s1 37 d1go3e1 not modelled 12.7 18 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 38 d2f23a2 not modelled 12.7 28 Fold:FKBP-like Superfamily:FKBP-like Family:GreA transcript cleavage factor, C-terminal domain 39 c2b8kG_ not modelled 12.5 13 PDB header:transferase Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kda PDBTitle: 12-subunit rna polymerase ii 40 d2oaia1 not modelled 12.0 17 Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like 41 d1hh2p1 not modelled 11.9 37 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 42 c3e0vB_ not modelled 11.7 25 PDB header:transferase Chain: B: PDB Molecule:pyruvate kinase; PDBTitle: crystal structure of pyruvate kinase from leishmania mexicana in2 complex with sulphate ions 43 d2plsa1 not modelled 11.6 8 Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like 44 d1nxza1 not modelled 11.3 19 Fold:PUA domain-like Superfamily:PUA domain-like Family:YggJ N-terminal domain-like 45 d1xnea_ not modelled 10.9 25 Fold:PUA domain-like Superfamily:PUA domain-like Family:ProFAR isomerase associated domain 46 c3h2yA_ not modelled 10.3 15 PDB header:hydrolase Chain: A: PDB Molecule:gtpase family protein; PDBTitle: crystal structure of yqeh gtpase from bacillus anthracis with dgdp2 bound 47 d1c0fa1 not modelled 10.2 20 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:Actin/HSP70 48 d2plia1 not modelled 10.0 25 Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like 49 d2c35b1 not modelled 9.7 16 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 50 c2xoaA_ not modelled 9.7 31 PDB header:metal transport Chain: A: PDB Molecule:ryanodine receptor 1; PDBTitle: crystal structure of the n-terminal three domains of the2 skeletal muscle ryanodine receptor (ryr1) 51 c3qr5B_ not modelled 9.6 31 PDB header:signaling protein Chain: B: PDB Molecule:cardiac ca2+ release channel; PDBTitle: structure of the first domain of a cardiac ryanodine receptor mutant2 with exon 3 deleted 52 d2rk5a1 not modelled 9.5 20 Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like 53 d2etna2 not modelled 9.4 28 Fold:FKBP-like Superfamily:FKBP-like Family:GreA transcript cleavage factor, C-terminal domain 54 c2cqoA_ not modelled 9.0 23 PDB header:ribosome Chain: A: PDB Molecule:nucleolar protein of 40 kda; PDBTitle: solution structure of the s1 rna binding domain of human2 hypothetical protein flj11067 55 c1xzzA_ not modelled 8.9 38 PDB header:membrane protein Chain: A: PDB Molecule:inositol 1,4,5-trisphosphate receptor type 1; PDBTitle: crystal structure of the ligand binding suppressor domain of type 12 inositol 1,4,5-trisphosphate receptor 56 d2q3za2 not modelled 8.2 25 Fold:Immunoglobulin-like beta-sandwich Superfamily:Transglutaminase, two C-terminal domains Family:Transglutaminase, two C-terminal domains 57 c1yz6A_ not modelled 8.2 20 PDB header:translation Chain: A: PDB Molecule:probable translation initiation factor 2 alpha PDBTitle: crystal structure of intact alpha subunit of aif2 from2 pyrococcus abyssi 58 d1q46a2 not modelled 8.1 20 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 59 c2z51A_ not modelled 7.8 14 PDB header:metal transport Chain: A: PDB Molecule:nifu-like protein 2, chloroplast; PDBTitle: crystal structure of arabidopsis cnfu involved in iron-2 sulfur cluster biosynthesis 60 d1hqia_ not modelled 7.2 22 Fold:Monooxygenase (hydroxylase) regulatory protein Superfamily:Monooxygenase (hydroxylase) regulatory protein Family:Monooxygenase (hydroxylase) regulatory protein 61 d1wi5a_ not modelled 7.2 24 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 62 d2asba1 not modelled 6.6 29 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 63 c2k52A_ not modelled 6.0 25 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein mj1198; PDBTitle: structure of uncharacterized protein mj1198 from2 methanocaldococcus jannaschii. northeast structural3 genomics target mjr117b 64 d1kl9a2 not modelled 6.0 20 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 65 c3t8sA_ not modelled 5.7 38 PDB header:transport protein, membrane protein Chain: A: PDB Molecule:inositol 1,4,5-trisphosphate receptor type 1; PDBTitle: apo and insp3-bound crystal structures of the ligand-binding domain of2 an insp3 receptor 66 c2c35F_ not modelled 5.7 16 PDB header:polymerase Chain: F: PDB Molecule:dna-directed rna polymerase ii 19 kda PDBTitle: subunits rpb4 and rpb7 of human rna polymerase ii 67 d2bf5a1 not modelled 5.6 17 Fold:Monooxygenase (hydroxylase) regulatory protein Superfamily:Monooxygenase (hydroxylase) regulatory protein Family:Monooxygenase (hydroxylase) regulatory protein 68 d1gdta1 not modelled 5.5 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 69 d1jmxa3 not modelled 5.5 30 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5 70 d2bf2a1 not modelled 5.5 17 Fold:Monooxygenase (hydroxylase) regulatory protein Superfamily:Monooxygenase (hydroxylase) regulatory protein Family:Monooxygenase (hydroxylase) regulatory protein 71 c3l6tB_ not modelled 5.3 42 PDB header:hydrolase Chain: B: PDB Molecule:mobilization protein trai; PDBTitle: crystal structure of an n-terminal mutant of the plasmid pcu1 trai2 relaxase domain 72 d1ttna1 not modelled 5.2 14 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 73 c1ttnA_ not modelled 5.2 14 PDB header:signaling protein Chain: A: PDB Molecule:dendritic cell-derived ubiquitin-like protein; PDBTitle: solution structure of the ubiquitin-like domain of human dc-2 ubp from dendritic cells 74 c2mobA_ not modelled 5.1 11 PDB header:oxidoreductase Chain: A: PDB Molecule:protein (methane monooxygenase regulatory PDBTitle: methane monooxygenase component b 75 d2moba_ not modelled 5.1 11 Fold:Monooxygenase (hydroxylase) regulatory protein Superfamily:Monooxygenase (hydroxylase) regulatory protein Family:Monooxygenase (hydroxylase) regulatory protein

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