Secondary structure and disorder prediction

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Sequence		M	E	K	R	T	P	H	T	R	L	S	Q	V	K	K	L	V	N	A	G	Q	V	R	T	T	R	S	A	L	L	N	A	D	E	L	G	L	D	F	D	G	M	C	N	V	I	I	G	L	S	E	S	D	F	Y	K	S	M	T	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?		?									?	?	?	?	?					?		?																				?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.
Sequence		Y	S	D	H	T	I	W	Q	D	V	Y	R	P	R	L	V	T	G	Q	V	Y	L	K	I	T	V	I	H	D	V	L	I	V	S	F	K	E	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 3hi2 chain D Region: 2 - 95 Aligned: 91 Modelled: 94 Confidence: 100.0% Identity: 100% PDB header:dna binding protein/toxin Chain: D: PDB Molecule:motility quorum-sensing regulator mqsr; PDBTitle: structure of the n-terminal domain of the e. coli antitoxin mqsa2 (ygit/b3021) in complex with the e. coli toxin mqsr (ygiu/b3022) Phyre2 PDB 3gqn chain A Region: 66 - 97 Aligned: 32 Modelled: 32 Confidence: 43.3% Identity: 19% PDB header:viral protein Chain: A: PDB Molecule:preneck appendage protein; PDBTitle: crystal structure of the pre-mature bacteriophage phi29 gene product2 12 Phyre2 PDB 2p6c chain B Region: 65 - 85 Aligned: 21 Modelled: 21 Confidence: 39.6% Identity: 24% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:aq_2013 protein; PDBTitle: crystal structure of hypothetical protein aq_2013 from aquifex2 aeolicus vf5. Phyre2 PDB 1ve0 chain A Region: 65 - 85 Aligned: 21 Modelled: 20 Confidence: 37.4% Identity: 19% PDB header:metal binding protein Chain: A: PDB Molecule:hypothetical protein (st2072); PDBTitle: crystal structure of uncharacterized protein st2072 from sulfolobus2 tokodaii Phyre2 PDB 1vmj chain A Region: 65 - 85 Aligned: 21 Modelled: 21 Confidence: 35.9% Identity: 24% Fold: YjbQ-like Superfamily: YjbQ-like Family: YjbQ-like Phyre2 PDB 2cu5 chain C Region: 65 - 84 Aligned: 20 Modelled: 20 Confidence: 34.3% Identity: 20% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:conserved hypothetical protein tt1486; PDBTitle: crystal structure of the conserved hypothetical protein tt1486 from2 thermus thermophilus hb8 Phyre2 PDB 2p6h chain B Region: 65 - 85 Aligned: 21 Modelled: 21 Confidence: 31.9% Identity: 19% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of hypothetical protein ape1520 from aeropyrum2 pernix k1 Phyre2 PDB 1vph chain A Region: 65 - 85 Aligned: 21 Modelled: 21 Confidence: 31.3% Identity: 19% Fold: YjbQ-like Superfamily: YjbQ-like Family: YjbQ-like Phyre2 PDB 1vmh chain A Region: 65 - 84 Aligned: 20 Modelled: 20 Confidence: 30.4% Identity: 30% Fold: YjbQ-like Superfamily: YjbQ-like Family: YjbQ-like Phyre2 PDB 2ga1 chain A domain 1 Region: 20 - 55 Aligned: 36 Modelled: 36 Confidence: 29.7% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Alr1493-like Phyre2 PDB 1vmf chain A Region: 65 - 85 Aligned: 21 Modelled: 21 Confidence: 25.7% Identity: 24% Fold: YjbQ-like Superfamily: YjbQ-like Family: YjbQ-like Phyre2 PDB 3gbg chain A Region: 7 - 59 Aligned: 53 Modelled: 53 Confidence: 23.2% Identity: 15% PDB header:transcription regulator Chain: A: PDB Molecule:tcp pilus virulence regulatory protein; PDBTitle: crystal structure of toxt from vibrio cholerae o395 Phyre2 PDB 2l4a chain A Region: 3 - 63 Aligned: 61 Modelled: 61 Confidence: 21.8% Identity: 18% PDB header:dna binding protein Chain: A: PDB Molecule:leucine responsive regulatory protein; PDBTitle: nmr structure of the dna-binding domain of e.coli lrp Phyre2 PDB 2ia9 chain A domain 1 Region: 57 - 77 Aligned: 21 Modelled: 19 Confidence: 21.3% Identity: 10% Fold: SpoVG-like Superfamily: SpoVG-like Family: SpoVG-like Phyre2 PDB 1jnp chain A Region: 62 - 84 Aligned: 23 Modelled: 23 Confidence: 20.4% Identity: 22% Fold: Oncogene products Superfamily: Oncogene products Family: Oncogene products Phyre2 PDB 2cg4 chain A domain 1 Region: 8 - 65 Aligned: 58 Modelled: 58 Confidence: 20.0% Identity: 5% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Lrp/AsnC-like transcriptional regulator N-terminal domain Phyre2 PDB 1bl0 chain A domain 2 Region: 9 - 58 Aligned: 50 Modelled: 50 Confidence: 19.3% Identity: 4% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: AraC type transcriptional activator Phyre2 PDB 2k9q chain B Region: 22 - 48 Aligned: 27 Modelled: 27 Confidence: 18.3% Identity: 26% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of hth_xre family transcriptional2 regulator bt_p548217 from bacteroides thetaiotaomicron.3 northeast structural genomics consortium target btr244. Phyre2 PDB 2i9x chain A domain 1 Region: 57 - 77 Aligned: 21 Modelled: 19 Confidence: 15.1% Identity: 10% Fold: SpoVG-like Superfamily: SpoVG-like Family: SpoVG-like Phyre2 PDB 1a1x chain A Region: 62 - 84 Aligned: 23 Modelled: 23 Confidence: 14.4% Identity: 22% Fold: Oncogene products Superfamily: Oncogene products Family: Oncogene products Phyre2 1 c3hi2D_ 2 c3gqnA_ 3 c2p6cB_ 4 c1ve0A_ 5 d1vmja_ 6 c2cu5C_ 7 c2p6hB_ 8 d1vpha_ 9 d1vmha_ 10 d2ga1a1 11 d1vmfa_ 12 c3gbgA_ 13 c2l4aA_ 14 d2ia9a1 15 d1jnpa_ 16 d2cg4a1 17 d1bl0a2 18 c2k9qB_ 19 d2i9xa1 20 d1a1xa_ 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

Detailed template information

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

1 c3hi2D_ 100.0 100 PDB header:dna binding protein/toxin Chain: D: PDB Molecule:motility quorum-sensing regulator mqsr; PDBTitle: structure of the n-terminal domain of the e. coli antitoxin mqsa2 (ygit/b3021) in complex with the e. coli toxin mqsr (ygiu/b3022) 2 c3gqnA_ 43.3 19 PDB header:viral protein Chain: A: PDB Molecule:preneck appendage protein; PDBTitle: crystal structure of the pre-mature bacteriophage phi29 gene product2 12 3 c2p6cB_ 39.6 24 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:aq_2013 protein; PDBTitle: crystal structure of hypothetical protein aq_2013 from aquifex2 aeolicus vf5. 4 c1ve0A_ 37.4 19 PDB header:metal binding protein Chain: A: PDB Molecule:hypothetical protein (st2072); PDBTitle: crystal structure of uncharacterized protein st2072 from sulfolobus2 tokodaii 5 d1vmja_ 35.9 24 Fold:YjbQ-like Superfamily:YjbQ-like Family:YjbQ-like 6 c2cu5C_ 34.3 20 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:conserved hypothetical protein tt1486; PDBTitle: crystal structure of the conserved hypothetical protein tt1486 from2 thermus thermophilus hb8 7 c2p6hB_ 31.9 19 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of hypothetical protein ape1520 from aeropyrum2 pernix k1 8 d1vpha_ 31.3 19 Fold:YjbQ-like Superfamily:YjbQ-like Family:YjbQ-like 9 d1vmha_ 30.4 30 Fold:YjbQ-like Superfamily:YjbQ-like Family:YjbQ-like 10 d2ga1a1 29.7 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Alr1493-like 11 d1vmfa_ 25.7 24 Fold:YjbQ-like Superfamily:YjbQ-like Family:YjbQ-like 12 c3gbgA_ 23.2 15 PDB header:transcription regulator Chain: A: PDB Molecule:tcp pilus virulence regulatory protein; PDBTitle: crystal structure of toxt from vibrio cholerae o395 13 c2l4aA_ 21.8 18 PDB header:dna binding protein Chain: A: PDB Molecule:leucine responsive regulatory protein; PDBTitle: nmr structure of the dna-binding domain of e.coli lrp 14 d2ia9a1 21.3 10 Fold:SpoVG-like Superfamily:SpoVG-like Family:SpoVG-like 15 d1jnpa_ 20.4 22 Fold:Oncogene products Superfamily:Oncogene products Family:Oncogene products 16 d2cg4a1 20.0 5 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 17 d1bl0a2 19.3 4 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 18 c2k9qB_ 18.3 26 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of hth_xre family transcriptional2 regulator bt_p548217 from bacteroides thetaiotaomicron.3 northeast structural genomics consortium target btr244. 19 d2i9xa1 15.1 10 Fold:SpoVG-like Superfamily:SpoVG-like Family:SpoVG-like 20 d1a1xa_ 14.4 22 Fold:Oncogene products Superfamily:Oncogene products Family:Oncogene products 21 c2knaA_ not modelled 14.4 16 PDB header:apoptosis Chain: A: PDB Molecule:baculoviral iap repeat-containing protein 4; PDBTitle: solution structure of uba domain of xiap 22 c2i9zB_ not modelled 14.3 10 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative septation protein spovg; PDBTitle: structural genomics, the crystal structure of full-length spovg from2 staphylococcus epidermidis atcc 12228 23 d1wi9a_ not modelled 13.1 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PCI domain (PINT motif) 24 d1d5ya2 not modelled 12.2 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 25 d1e8ca3 not modelled 11.8 20 Fold:Ribokinase-like Superfamily:MurD-like peptide ligases, catalytic domain Family:MurCDEF 26 d1jsga_ not modelled 10.7 25 Fold:Oncogene products Superfamily:Oncogene products Family:Oncogene products 27 c3beyC_ not modelled 9.4 21 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:conserved protein o27018; PDBTitle: crystal structure of the protein o27018 from methanobacterium2 thermoautotrophicum. northeast structural genomics consortium target3 tt217 28 d1ixsa_ not modelled 9.3 21 Fold:RuvA C-terminal domain-like Superfamily:DNA helicase RuvA subunit, C-terminal domain Family:DNA helicase RuvA subunit, C-terminal domain 29 c2vn2B_ not modelled 8.6 16 PDB header:replication Chain: B: PDB Molecule:chromosome replication initiation protein; PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426 30 d1wspa1 not modelled 8.0 11 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:DIX domain 31 d1a9xa1 not modelled 8.0 11 Fold:Carbamoyl phosphate synthetase, large subunit connection domain Superfamily:Carbamoyl phosphate synthetase, large subunit connection domain Family:Carbamoyl phosphate synthetase, large subunit connection domain 32 d1au7a2 not modelled 8.0 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain 33 c2f4qA_ not modelled 8.0 21 PDB header:isomerase Chain: A: PDB Molecule:type i topoisomerase, putative; PDBTitle: crystal structure of deinococcus radiodurans topoisomerase ib 34 c1xofB_ not modelled 7.9 18 PDB header:de novo protein Chain: B: PDB Molecule:bbahett1; PDBTitle: heterooligomeric beta beta alpha miniprotein 35 c3gqhB_ not modelled 7.9 19 PDB header:viral protein Chain: B: PDB Molecule:preneck appendage protein; PDBTitle: crystal structure of the bacteriophage phi29 gene product2 12 c-terminal fragment 36 c2v79B_ not modelled 7.7 10 PDB header:dna-binding protein Chain: B: PDB Molecule:dna replication protein dnad; PDBTitle: crystal structure of the n-terminal domain of dnad from2 bacillus subtilis 37 d2f5ga1 not modelled 7.3 14 Fold:Ferredoxin-like Superfamily:Transposase IS200-like Family:Transposase IS200-like 38 c1ezeA_ not modelled 6.2 30 PDB header:transferase inhibitor Chain: A: PDB Molecule:cholesteryl ester transferase inhibitor protein; PDBTitle: structural studies of a baboon (papio sp.) plasma protein2 inhibitor of cholesteryl ester transferase. 39 d1q08a_ not modelled 6.0 18 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 40 c3r0aB_ not modelled 6.0 15 PDB header:transcription regulator Chain: B: PDB Molecule:putative transcriptional regulator; PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196) 41 d1e3oc2 not modelled 5.8 20 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain 42 c2abjG_ not modelled 5.6 27 PDB header:transferase Chain: G: PDB Molecule:branched-chain-amino-acid aminotransferase, cytosolic; PDBTitle: crystal structure of human branched chain amino acid transaminase in a2 complex with an inhibitor, c16h10n2o4f3scl, and pyridoxal 5'3 phosphate. 43 c1nzeA_ not modelled 5.6 12 PDB header:oxidoreductase Chain: A: PDB Molecule:oxygen-evolving enhancer protein 3; PDBTitle: crystal structure of psbq polypeptide of photosystem ii2 from higher plants 44 d1nzea_ not modelled 5.6 12 Fold:Four-helical up-and-down bundle Superfamily:Oxygen-evolving enhancer protein 3, Family:Oxygen-evolving enhancer protein 3, 45 d2hkua2 not modelled 5.5 20 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 46 d2h7aa1 not modelled 5.3 19 Fold:YcgL-like Superfamily:YcgL-like Family:YcgL-like 47 d2hqya2 not modelled 5.2 32 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:FemXAB nonribosomal peptidyltransferases 48 d1bhga2 not modelled 5.2 12 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:beta-Galactosidase/glucuronidase, N-terminal domain 49 c1hjpA_ not modelled 5.2 11 PDB header:dna recombination Chain: A: PDB Molecule:ruva; PDBTitle: holliday junction binding protein ruva from e. coli 50 d2vzsa4 not modelled 5.1 21 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:beta-Galactosidase/glucuronidase, N-terminal domain

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