Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	H	Q	Q	H	M	R	N	I	A	Q	W	L	Q	E	N	G	I	T	R	A	T	V	A	P	D	W	M	S	I	P	C	G	F	M	A	C	D	A	Q	R	V	I	C	R	I	D	E	C	R	G	W	S	A	G	L	A	L	A
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		P	V	M	F	R	A	Q	L	N	E	Q	D	L	P	L	S	L	T	V	V	G	I	A	P	E	K	L	S	A	W	A	G	A	D	A	E	R	L	T	V	T	A	L	P	A	I	T	T	Y	G	E	P	E	G	N	L	L	T	G	P
Secondary structure
SS confidence
Disorder																									?		?	?	?	?	?	?				?		?	?	?	?						?	?	?	?										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		W	Q	P	R	V	S	Y	R	K	Q	W	A	R	W	R	V	M	I	L	P	I	L	L	I	L	V	A	L	A	V	E	R	G	V	T	L	W	S	V	S	E	Q	V	A	Q	S	R	T	Q	A	E	E	Q	F	L	T	L	F	P	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		Q	K	R	I	V	N	L	R	S	Q	V	T	M	A	L	K	K	Y	R	P	Q	A	D	D	T	R	L	L	A	E	L	S	A	I	A	S	T	L	K	S	A	S	L	S	D	I	E	M	R	G	F	T	F	D	Q	K	R	Q	I	L
Secondary structure
SS confidence
Disorder			?	?	?	?													?	?	?	?	?	?	?	?	?												?	?	?	?	?	?	?	?								?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.
Sequence		H	L	Q	L	R	A	A	N	F	A	S	F	D	K	L	R	S	V	L	A	T	D	Y	V	V	Q	Q	D	A	L	Q	K	E	G	D	A	V	S	G	G	V	T	L	R	R	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 1yf5 chain L Region: 1 - 122 Aligned: 122 Modelled: 122 Confidence: 99.9% Identity: 16% PDB header:transport protein Chain: L: PDB Molecule:general secretion pathway protein l; PDBTitle: cyto-epsl: the cytoplasmic domain of epsl, an inner membrane component2 of the type ii secretion system of vibrio cholerae Phyre2 PDB 2w7v chain B Region: 202 - 286 Aligned: 82 Modelled: 85 Confidence: 99.8% Identity: 29% PDB header:transport protein Chain: B: PDB Molecule:general secretion pathway protein l; PDBTitle: periplasmic domain of epsl from vibrio parahaemolyticus Phyre2 PDB 2bh1 chain A domain 1 Region: 35 - 122 Aligned: 88 Modelled: 88 Confidence: 99.6% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Actin-like ATPase domain Family: Cyto-EpsL domain Phyre2 PDB 1uv7 chain A Region: 228 - 285 Aligned: 56 Modelled: 58 Confidence: 78.8% Identity: 11% Fold: RRF/tRNA synthetase additional domain-like Superfamily: General secretion pathway protein M, EpsM Family: General secretion pathway protein M, EpsM Phyre2 PDB 1uv7 chain A Region: 228 - 285 Aligned: 56 Modelled: 58 Confidence: 78.8% Identity: 11% PDB header:transport Chain: A: PDB Molecule:general secretion pathway protein m; PDBTitle: periplasmic domain of epsm from vibrio cholerae Phyre2 PDB 2l3m chain A Region: 212 - 266 Aligned: 50 Modelled: 55 Confidence: 33.8% Identity: 20% PDB header:metal binding protein Chain: A: PDB Molecule:copper-ion-binding protein; PDBTitle: solution structure of the putative copper-ion-binding protein from2 bacillus anthracis str. ames Phyre2 PDB 1p6t chain A domain 2 Region: 212 - 276 Aligned: 60 Modelled: 65 Confidence: 29.6% Identity: 12% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 2aw0 chain A Region: 212 - 267 Aligned: 51 Modelled: 56 Confidence: 27.1% Identity: 10% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 1cpz chain A Region: 212 - 267 Aligned: 51 Modelled: 56 Confidence: 21.5% Identity: 12% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 1s6u chain A Region: 228 - 273 Aligned: 45 Modelled: 46 Confidence: 20.9% Identity: 4% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 1sb6 chain A Region: 212 - 266 Aligned: 47 Modelled: 55 Confidence: 20.5% Identity: 13% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 2kt2 chain A Region: 228 - 270 Aligned: 41 Modelled: 43 Confidence: 17.9% Identity: 15% PDB header:oxidoreductase Chain: A: PDB Molecule:mercuric reductase; PDBTitle: structure of nmera, the n-terminal hma domain of tn501 mercuric2 reductase Phyre2 PDB 2jpi chain A Region: 232 - 263 Aligned: 32 Modelled: 32 Confidence: 17.3% Identity: 13% PDB header:structural genomics Chain: A: PDB Molecule:hypothetical protein; PDBTitle: chemical shift assignments of pa4090 from pseudomonas2 aeruginosa Phyre2 PDB 1p6t chain A domain 1 Region: 212 - 265 Aligned: 49 Modelled: 54 Confidence: 17.1% Identity: 10% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 2qif chain A domain 1 Region: 212 - 265 Aligned: 49 Modelled: 54 Confidence: 16.0% Identity: 12% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 1f44 chain A domain 1 Region: 4 - 30 Aligned: 27 Modelled: 27 Confidence: 14.5% Identity: 19% Fold: SAM domain-like Superfamily: lambda integrase-like, N-terminal domain Family: lambda integrase-like, N-terminal domain Phyre2 PDB 2k2p chain A Region: 212 - 266 Aligned: 47 Modelled: 55 Confidence: 14.4% Identity: 6% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atu1203; PDBTitle: solution nmr structure of protein atu1203 from agrobacterium2 tumefaciens. northeast structural genomics consortium (nesg) target3 att10, ontario center for structural proteomics target atc1183 Phyre2 PDB 3dxs chain X Region: 212 - 267 Aligned: 51 Modelled: 56 Confidence: 13.7% Identity: 4% PDB header:hydrolase Chain: X: PDB Molecule:copper-transporting atpase ran1; PDBTitle: crystal structure of a copper binding domain from hma7, a p-2 type atpase Phyre2 PDB 1mwz chain A Region: 228 - 272 Aligned: 42 Modelled: 45 Confidence: 13.5% Identity: 10% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 1j5y chain A domain 2 Region: 243 - 267 Aligned: 25 Modelled: 25 Confidence: 13.2% Identity: 8% Fold: HPr-like Superfamily: Putative transcriptional regulator TM1602, C-terminal domain Family: Putative transcriptional regulator TM1602, C-terminal domain Phyre2 1 c1yf5L_ 2 c2w7vB_ 3 d2bh1a1 4 d1uv7a_ 5 c1uv7A_ 6 c2l3mA_ 7 d1p6ta2 8 d2aw0a_ 9 d1cpza_ 10 d1s6ua_ 11 d1sb6a_ 12 c2kt2A_ 13 c2jpiA_ 14 d1p6ta1 15 d2qifa1 16 d1f44a1 17 c2k2pA_ 18 c3dxsX_ 19 d1mwza_ 20 d1j5ya2 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

Detailed template information

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

1 c1yf5L_ 99.9 16 PDB header:transport protein Chain: L: PDB Molecule:general secretion pathway protein l; PDBTitle: cyto-epsl: the cytoplasmic domain of epsl, an inner membrane component2 of the type ii secretion system of vibrio cholerae 2 c2w7vB_ 99.8 29 PDB header:transport protein Chain: B: PDB Molecule:general secretion pathway protein l; PDBTitle: periplasmic domain of epsl from vibrio parahaemolyticus 3 d2bh1a1 99.6 15 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:Cyto-EpsL domain 4 d1uv7a_ 78.8 11 Fold:RRF/tRNA synthetase additional domain-like Superfamily:General secretion pathway protein M, EpsM Family:General secretion pathway protein M, EpsM 5 c1uv7A_ 78.8 11 PDB header:transport Chain: A: PDB Molecule:general secretion pathway protein m; PDBTitle: periplasmic domain of epsm from vibrio cholerae 6 c2l3mA_ 33.8 20 PDB header:metal binding protein Chain: A: PDB Molecule:copper-ion-binding protein; PDBTitle: solution structure of the putative copper-ion-binding protein from2 bacillus anthracis str. ames 7 d1p6ta2 29.6 12 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 8 d2aw0a_ 27.1 10 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 9 d1cpza_ 21.5 12 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 10 d1s6ua_ 20.9 4 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 11 d1sb6a_ 20.5 13 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 12 c2kt2A_ 17.9 15 PDB header:oxidoreductase Chain: A: PDB Molecule:mercuric reductase; PDBTitle: structure of nmera, the n-terminal hma domain of tn501 mercuric2 reductase 13 c2jpiA_ 17.3 13 PDB header:structural genomics Chain: A: PDB Molecule:hypothetical protein; PDBTitle: chemical shift assignments of pa4090 from pseudomonas2 aeruginosa 14 d1p6ta1 17.1 10 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 15 d2qifa1 16.0 12 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 16 d1f44a1 14.5 19 Fold:SAM domain-like Superfamily:lambda integrase-like, N-terminal domain Family:lambda integrase-like, N-terminal domain 17 c2k2pA_ 14.4 6 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atu1203; PDBTitle: solution nmr structure of protein atu1203 from agrobacterium2 tumefaciens. northeast structural genomics consortium (nesg) target3 att10, ontario center for structural proteomics target atc1183 18 c3dxsX_ 13.7 4 PDB header:hydrolase Chain: X: PDB Molecule:copper-transporting atpase ran1; PDBTitle: crystal structure of a copper binding domain from hma7, a p-2 type atpase 19 d1mwza_ 13.5 10 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 20 d1j5ya2 13.2 8 Fold:HPr-like Superfamily:Putative transcriptional regulator TM1602, C-terminal domain Family:Putative transcriptional regulator TM1602, C-terminal domain 21 c1yg0A_ not modelled 12.9 14 PDB header:metal transport Chain: A: PDB Molecule:cop associated protein; PDBTitle: solution structure of apo-copp from helicobacter pylori 22 c2x29A_ not modelled 11.9 22 PDB header:cell adhesion Chain: A: PDB Molecule:tumor necrosis factor ligand superfamily member PDBTitle: crystal structure of human4-1bb ligand ectodomain 23 d1kvja_ not modelled 11.5 4 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 24 c3hd7A_ not modelled 11.1 12 PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 25 d2ggpb1 not modelled 10.7 3 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 26 c2gcfA_ not modelled 9.8 5 PDB header:hydrolase Chain: A: PDB Molecule:cation-transporting atpase pacs; PDBTitle: solution structure of the n-terminal domain of the coppper(i) atpase2 pacs in its apo form 27 c3ibwA_ not modelled 9.6 17 PDB header:transferase Chain: A: PDB Molecule:gtp pyrophosphokinase; PDBTitle: crystal structure of the act domain from gtp2 pyrophosphokinase of chlorobium tepidum. northeast3 structural genomics consortium target ctr148a 28 c2rrlA_ not modelled 9.4 16 PDB header:protein transport Chain: A: PDB Molecule:flagellar hook-length control protein; PDBTitle: solution structure of the c-terminal domain of the flik 29 d1je3a_ not modelled 9.2 15 Fold:IF3-like Superfamily:SirA-like Family:SirA-like 30 c2kyzA_ not modelled 9.1 15 PDB header:metal binding protein Chain: A: PDB Molecule:heavy metal binding protein; PDBTitle: nmr structure of heavy metal binding protein tm0320 from thermotoga2 maritima 31 d2vzsa2 not modelled 9.0 15 Fold:Immunoglobulin-like beta-sandwich Superfamily:beta-Galactosidase/glucuronidase domain Family:beta-Galactosidase/glucuronidase domain 32 c2ofhX_ not modelled 9.0 11 PDB header:hydrolase, membrane protein Chain: X: PDB Molecule:zinc-transporting atpase; PDBTitle: solution structure of the n-terminal domain of the zinc(ii) atpase2 ziaa in its apo form 33 c2yciX_ not modelled 8.8 16 PDB header:transferase Chain: X: PDB Molecule:5-methyltetrahydrofolate corrinoid/iron sulfur protein PDBTitle: methyltransferase native 34 d1osda_ not modelled 8.3 12 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 35 c2l3wA_ not modelled 7.7 7 PDB header:photosynthesis Chain: A: PDB Molecule:phycobilisome rod linker polypeptide; PDBTitle: solution nmr structure of the pbs linker domain of phycobilisome rod2 linker polypeptide from synechococcus elongatus, northeast structural3 genomics consortium target snr168a 36 c3h0dB_ not modelled 7.5 25 PDB header:transcription/dna Chain: B: PDB Molecule:ctsr; PDBTitle: crystal structure of ctsr in complex with a 26bp dna duplex 37 d1afia_ not modelled 7.3 15 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 38 c3k13A_ not modelled 7.2 9 PDB header:transferase Chain: A: PDB Molecule:5-methyltetrahydrofolate-homocysteine methyltransferase; PDBTitle: structure of the pterin-binding domain metr of 5-2 methyltetrahydrofolate-homocysteine methyltransferase from3 bacteroides thetaiotaomicron 39 c1yjrA_ not modelled 7.1 3 PDB header:hydrolase Chain: A: PDB Molecule:copper-transporting atpase 1; PDBTitle: solution structure of the apo form of the sixth soluble2 domain a69p mutant of menkes protein 40 c3fryB_ not modelled 7.1 14 PDB header:hydrolase Chain: B: PDB Molecule:probable copper-exporting p-type atpase a; PDBTitle: crystal structure of the copa c-terminal metal binding domain 41 c3nklA_ not modelled 6.9 14 PDB header:oxidoreductase/lyase Chain: A: PDB Molecule:udp-d-quinovosamine 4-dehydrogenase; PDBTitle: crystal structure of udp-d-quinovosamine 4-dehydrogenase from vibrio2 fischeri 42 c2rjzA_ not modelled 6.9 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:pilo protein; PDBTitle: crystal structure of the type 4 fimbrial biogenesis protein pilo from2 pseudomonas aeruginosa 43 c2ldiA_ not modelled 6.5 11 PDB header:hydrolase Chain: A: PDB Molecule:zinc-transporting atpase; PDBTitle: nmr solution structure of ziaan sub mutant 44 c2ropA_ not modelled 6.5 14 PDB header:hydrolase Chain: A: PDB Molecule:copper-transporting atpase 2; PDBTitle: solution structure of domains 3 and 4 of human atp7b 45 c2ychA_ not modelled 6.5 10 PDB header:cell cycle Chain: A: PDB Molecule:competence protein pilm; PDBTitle: pilm-piln type iv pilus biogenesis complex 46 d1q8la_ not modelled 6.2 5 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 47 c1y3kA_ not modelled 5.8 8 PDB header:hydrolase Chain: A: PDB Molecule:copper-transporting atpase 1; PDBTitle: solution structure of the apo form of the fifth domain of2 menkes protein 48 c2k42B_ not modelled 5.4 30 PDB header:signaling protein Chain: B: PDB Molecule:espfu; PDBTitle: solution structure of the gtpase binding domain of wasp in2 complex with espfu, an ehec effector 49 d1t1ea2 not modelled 5.1 10 Fold:Ferredoxin-like Superfamily:Protease propeptides/inhibitors Family:Subtilase propeptides/inhibitors

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