Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	E	W	S	G	E	Y	I	S	P	Y	A	E	H	G	K	K	S	E	Q	V	K	K	I	T	V	S	I	P	L	K	V	L	K	I	L	T	D	E	R	T	R	R	Q	V	N	N	L	R	H	A	T	N	S	E	L	L	C	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?										?	?	?	?	?		?	?																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.
Sequence		A	F	L	H	A	F	T	G	Q	P	L	P	D	D	A	D	L	R	K	E	R	S	D	E	I	P	E	A	A	K	E	I	M	R	E	M	G	I	N	P	E	T	W	E	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 1cmc chain A Region: 2 - 105 Aligned: 104 Modelled: 104 Confidence: 100.0% Identity: 100% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: Met repressor, MetJ (MetR) Phyre2 PDB 1is7 chain F Region: 72 - 101 Aligned: 30 Modelled: 30 Confidence: 35.6% Identity: 20% PDB header:hydrolase/protein binding Chain: F: PDB Molecule:gtp cyclohydrolase i; PDBTitle: crystal structure of rat gtpchi/gfrp stimulatory complex Phyre2 PDB 1wpl chain A Region: 72 - 101 Aligned: 30 Modelled: 30 Confidence: 35.6% Identity: 20% Fold: T-fold Superfamily: Tetrahydrobiopterin biosynthesis enzymes-like Family: GTP cyclohydrolase I Phyre2 PDB 1n3l chain A Region: 63 - 101 Aligned: 38 Modelled: 39 Confidence: 27.2% Identity: 21% Fold: Adenine nucleotide alpha hydrolase-like Superfamily: Nucleotidylyl transferase Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain Phyre2 PDB 2pu9 chain B domain 1 Region: 1 - 11 Aligned: 11 Modelled: 11 Confidence: 25.6% Identity: 45% Fold: SH3-like barrel Superfamily: Electron transport accessory proteins Family: Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain Phyre2 PDB 2fek chain A Region: 58 - 103 Aligned: 46 Modelled: 46 Confidence: 25.6% Identity: 15% PDB header:hydrolase Chain: A: PDB Molecule:low molecular weight protein-tyrosine- PDBTitle: structure of a protein tyrosine phosphatase Phyre2 PDB 2wmy chain H Region: 58 - 103 Aligned: 46 Modelled: 46 Confidence: 24.1% Identity: 13% PDB header:hydrolase Chain: H: PDB Molecule:putative acid phosphatase wzb; PDBTitle: crystal structure of the tyrosine phosphatase wzb from2 escherichia coli k30 in complex with sulphate. Phyre2 PDB 1q11 chain A Region: 63 - 101 Aligned: 38 Modelled: 39 Confidence: 18.3% Identity: 21% PDB header:ligase Chain: A: PDB Molecule:tyrosyl-trna synthetase; PDBTitle: crystal structure of an active fragment of human tyrosyl-trna2 synthetase with tyrosinol Phyre2 PDB 2if6 chain A domain 1 Region: 55 - 102 Aligned: 41 Modelled: 48 Confidence: 17.9% Identity: 32% Fold: Cysteine proteinases Superfamily: Cysteine proteinases Family: YiiX-like Phyre2 PDB 2j5b chain A Region: 63 - 101 Aligned: 35 Modelled: 39 Confidence: 16.1% Identity: 20% PDB header:ligase Chain: A: PDB Molecule:tyrosyl-trna synthetase; PDBTitle: structure of the tyrosyl trna synthetase from acanthamoeba2 polyphaga mimivirus complexed with tyrosynol Phyre2 PDB 2k29 chain A Region: 82 - 102 Aligned: 21 Modelled: 21 Confidence: 14.7% Identity: 24% PDB header:transcription Chain: A: PDB Molecule:antitoxin relb; PDBTitle: structure of the dbd domain of e. coli antitoxin relb Phyre2 PDB 1txl chain A Region: 1 - 13 Aligned: 13 Modelled: 13 Confidence: 14.5% Identity: 31% Fold: Lipocalins Superfamily: Lipocalins Family: Hypothetical protein YodA Phyre2 PDB 1txl chain A Region: 1 - 13 Aligned: 13 Modelled: 13 Confidence: 14.5% Identity: 31% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:metal-binding protein yoda; PDBTitle: crystal structure of metal-binding protein yoda from e.2 coli, pfam duf149 Phyre2 PDB 2y69 chain Q Region: 57 - 100 Aligned: 38 Modelled: 44 Confidence: 14.5% Identity: 18% PDB header:electron transport Chain: Q: PDB Molecule:cytochrome c oxidase subunit 4 isoform 1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1q8d chain A Region: 54 - 70 Aligned: 17 Modelled: 17 Confidence: 13.5% Identity: 29% Fold: GDNF receptor-like Superfamily: GDNF receptor-like Family: GDNF receptor-like Phyre2 PDB 2d5r chain A domain 1 Region: 62 - 100 Aligned: 39 Modelled: 39 Confidence: 13.5% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: CAF1-like ribonuclease Phyre2 PDB 2dlc chain X Region: 63 - 101 Aligned: 38 Modelled: 39 Confidence: 13.1% Identity: 24% PDB header:ligase/trna Chain: X: PDB Molecule:tyrosyl-trna synthetase, cytoplasmic; PDBTitle: crystal structure of the ternary complex of yeast tyrosyl-trna2 synthetase Phyre2 PDB 1v54 chain D Region: 57 - 100 Aligned: 38 Modelled: 44 Confidence: 12.6% Identity: 18% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit IV Family: Mitochondrial cytochrome c oxidase subunit IV Phyre2 PDB 1qcs chain A domain 2 Region: 54 - 71 Aligned: 18 Modelled: 17 Confidence: 11.2% Identity: 17% Fold: Cdc48 domain 2-like Superfamily: Cdc48 domain 2-like Family: Cdc48 domain 2-like Phyre2 PDB 2bj7 chain A domain 1 Region: 21 - 48 Aligned: 28 Modelled: 28 Confidence: 10.6% Identity: 21% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 1 d1cmca_ 2 c1is7F_ 3 d1wpla_ 4 d1n3la_ 5 d2pu9b1 6 c2fekA_ 7 c2wmyH_ 8 c1q11A_ 9 d2if6a1 10 c2j5bA_ 11 c2k29A_ 12 d1txla_ 13 c1txlA_ 14 c2y69Q_ 15 d1q8da_ 16 d2d5ra1 17 c2dlcX_ 18 d1v54d_ 19 d1qcsa2 20 d2bj7a1 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

Detailed template information

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

1 d1cmca_ 100.0 100 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Met repressor, MetJ (MetR) 2 c1is7F_ 35.6 20 PDB header:hydrolase/protein binding Chain: F: PDB Molecule:gtp cyclohydrolase i; PDBTitle: crystal structure of rat gtpchi/gfrp stimulatory complex 3 d1wpla_ 35.6 20 Fold:T-fold Superfamily:Tetrahydrobiopterin biosynthesis enzymes-like Family:GTP cyclohydrolase I 4 d1n3la_ 27.2 21 Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain 5 d2pu9b1 25.6 45 Fold:SH3-like barrel Superfamily:Electron transport accessory proteins Family:Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain 6 c2fekA_ 25.6 15 PDB header:hydrolase Chain: A: PDB Molecule:low molecular weight protein-tyrosine- PDBTitle: structure of a protein tyrosine phosphatase 7 c2wmyH_ 24.1 13 PDB header:hydrolase Chain: H: PDB Molecule:putative acid phosphatase wzb; PDBTitle: crystal structure of the tyrosine phosphatase wzb from2 escherichia coli k30 in complex with sulphate. 8 c1q11A_ 18.3 21 PDB header:ligase Chain: A: PDB Molecule:tyrosyl-trna synthetase; PDBTitle: crystal structure of an active fragment of human tyrosyl-trna2 synthetase with tyrosinol 9 d2if6a1 17.9 32 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:YiiX-like 10 c2j5bA_ 16.1 20 PDB header:ligase Chain: A: PDB Molecule:tyrosyl-trna synthetase; PDBTitle: structure of the tyrosyl trna synthetase from acanthamoeba2 polyphaga mimivirus complexed with tyrosynol 11 c2k29A_ 14.7 24 PDB header:transcription Chain: A: PDB Molecule:antitoxin relb; PDBTitle: structure of the dbd domain of e. coli antitoxin relb 12 d1txla_ 14.5 31 Fold:Lipocalins Superfamily:Lipocalins Family:Hypothetical protein YodA 13 c1txlA_ 14.5 31 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:metal-binding protein yoda; PDBTitle: crystal structure of metal-binding protein yoda from e.2 coli, pfam duf149 14 c2y69Q_ 14.5 18 PDB header:electron transport Chain: Q: PDB Molecule:cytochrome c oxidase subunit 4 isoform 1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 15 d1q8da_ 13.5 29 Fold:GDNF receptor-like Superfamily:GDNF receptor-like Family:GDNF receptor-like 16 d2d5ra1 13.5 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:CAF1-like ribonuclease 17 c2dlcX_ 13.1 24 PDB header:ligase/trna Chain: X: PDB Molecule:tyrosyl-trna synthetase, cytoplasmic; PDBTitle: crystal structure of the ternary complex of yeast tyrosyl-trna2 synthetase 18 d1v54d_ 12.6 18 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit IV Family:Mitochondrial cytochrome c oxidase subunit IV 19 d1qcsa2 11.2 17 Fold:Cdc48 domain 2-like Superfamily:Cdc48 domain 2-like Family:Cdc48 domain 2-like 20 d2bj7a1 10.6 21 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 21 d1a8ra_ not modelled 9.6 22 Fold:T-fold Superfamily:Tetrahydrobiopterin biosynthesis enzymes-like Family:GTP cyclohydrolase I 22 d1ioka2 not modelled 9.2 44 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 23 c3idwA_ not modelled 9.1 25 PDB header:endocytosis Chain: A: PDB Molecule:actin cytoskeleton-regulatory complex protein sla1; PDBTitle: crystal structure of sla1 homology domain 2 24 c2v5eA_ not modelled 8.7 29 PDB header:receptor/glycoprotein complex Chain: A: PDB Molecule:gdnf family receptor alpha-1; PDBTitle: the structure of the gdnf\:coreceptor complex\: insights2 into ret signalling and heparin binding. 25 c3fubA_ not modelled 8.6 29 PDB header:hormone Chain: A: PDB Molecule:gdnf family receptor alpha-1; PDBTitle: crystal structure of gdnf-gfralpha1 complex 26 d2hafa1 not modelled 8.5 27 Fold:VC0467-like Superfamily:VC0467-like Family:VC0467-like 27 d2gf5a1 not modelled 8.4 17 Fold:DEATH domain Superfamily:DEATH domain Family:DEATH domain, DD 28 c1qdnA_ not modelled 8.3 17 PDB header:fusion protein Chain: A: PDB Molecule:protein (n-ethylmaleimide sensitive fusion PDBTitle: amino terminal domain of the n-ethylmaleimide sensitive2 fusion protein (nsf) 29 c2cycB_ not modelled 8.2 18 PDB header:ligase Chain: B: PDB Molecule:tyrosyl-trna synthetase; PDBTitle: crystal structure of tyrosyl-trna synthetase complexed with l-tyrosine2 from pyrococcus horikoshii 30 d1jf8a_ not modelled 8.2 16 Fold:Phosphotyrosine protein phosphatases I-like Superfamily:Phosphotyrosine protein phosphatases I Family:Low-molecular-weight phosphotyrosine protein phosphatases 31 c2l18A_ not modelled 7.8 18 PDB header:oxidoreductase Chain: A: PDB Molecule:arsenate reductase; PDBTitle: an arsenate reductase in the phosphate binding state 32 d1sjpa2 not modelled 7.8 44 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 33 d1h8ba_ not modelled 7.7 21 Fold:EF Hand-like Superfamily:EF-hand Family:EF-hand modules in multidomain proteins 34 d1sbxa_ not modelled 7.7 50 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Dachshund-homology domain 35 d1wr6a1 not modelled 7.6 26 Fold:Spectrin repeat-like Superfamily:GAT-like domain Family:GAT domain 36 c3fwcN_ not modelled 7.3 23 PDB header:cell cycle, transcription Chain: N: PDB Molecule:nuclear mrna export protein sac3; PDBTitle: sac3:sus1:cdc31 complex 37 d1dk7a_ not modelled 7.1 44 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 38 d1srva_ not modelled 7.1 56 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 39 d1oela2 not modelled 6.5 44 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 40 d1we3a2 not modelled 6.4 56 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 41 d1np3a1 not modelled 6.2 33 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:Acetohydroxy acid isomeroreductase (ketol-acid reductoisomerase, KARI) 42 d1xrsb2 not modelled 6.1 50 Fold:Dodecin subunit-like Superfamily:D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain Family:D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain 43 c2aj2A_ not modelled 6.0 27 PDB header:unknown function Chain: A: PDB Molecule:hypothetical upf0301 protein vc0467; PDBTitle: x-ray crystal structure of protein vc0467 from vibrio2 cholerae. northeast structural genomics consortium target3 vcr8. 44 c2p51A_ not modelled 5.9 32 PDB header:hydrolase, gene regulation Chain: A: PDB Molecule:spcc18.06c protein; PDBTitle: crystal structure of the s. pombe pop2p deadenylation2 subunit 45 c1v91A_ not modelled 5.7 71 PDB header:toxin Chain: A: PDB Molecule:delta-palutoxin it2; PDBTitle: solution structure of insectidal toxin delta-paluit2-nh2 46 d2dofa1 not modelled 5.7 13 Fold:Another 3-helical bundle Superfamily:FF domain Family:FF domain 47 d1wu2a2 not modelled 5.6 36 Fold:MoeA N-terminal region -like Superfamily:MoeA N-terminal region -like Family:MoeA N-terminal region -like 48 c3t38B_ not modelled 5.5 33 PDB header:oxidoreductase Chain: B: PDB Molecule:arsenate reductase; PDBTitle: corynebacterium glutamicum thioredoxin-dependent arsenate reductase2 cg_arsc1' 49 d2bnma1 not modelled 5.4 29 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 50 c2cyaA_ not modelled 5.4 22 PDB header:ligase Chain: A: PDB Molecule:tyrosyl-trna synthetase; PDBTitle: crystal structure of tyrosyl-trna synthetase from aeropyrum pernix 51 d1sjpa3 not modelled 5.3 0 Fold:GroEL-intermediate domain like Superfamily:GroEL-intermediate domain like Family:GroEL-like chaperone, intermediate domain 52 d1wrda1 not modelled 5.2 17 Fold:Spectrin repeat-like Superfamily:GAT-like domain Family:GAT domain 53 d2cyua1 not modelled 5.2 11 Fold:Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex Superfamily:Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex Family:Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 54 d2nqra2 not modelled 5.0 36 Fold:MoeA N-terminal region -like Superfamily:MoeA N-terminal region -like Family:MoeA N-terminal region -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

---

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