Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	T	F	G	A	C	R	F	F	F	G	Y	P	V	V	T	N	I	F	S	L	W	R	D	D	G	R	A	S	C	G	Y	N	K	T	M	R	F	Y	M	R	K	I	K	G	L	R	W	Y	M	I	A	L	V	T	L	G	T	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?													?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	G	Y	L	T	R	N	T	V	A	A	A	A	P	T	L	M	E	E	L	N	I	S	T	Q	Q	Y	S	Y	I	I	A	A	Y	S	A	A	Y	T	V	M	Q	P	V	A	G	Y	V	L	D	V	L	G	T	K	I	G	Y	A	M
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		F	A	V	L	W	A	V	F	C	G	A	T	A	L	A	G	S	W	G	G	L	A	V	A	R	G	A	V	G	A	A	E	A	A	M	I	P	A	G	L	K	A	S	S	E	W	F	P	A	K	E	R	S	I	A	V	G	Y	F	N
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	G	S	S	I	G	A	M	I	A	P	P	L	V	V	W	A	I	V	M	H	S	W	Q	M	A	F	I	I	S	G	A	L	S	F	I	W	A	M	A	W	L	I	F	Y	K	H	P	R	D	Q	K	H	L	T	D	E	E	R	D
Secondary structure
SS confidence
Disorder																																																					?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		Y	I	I	N	G	Q	E	A	Q	H	Q	V	S	T	A	K	K	M	S	V	G	Q	I	L	R	N	R	Q	F	W	G	I	A	L	P	R	F	L	A	E	P	A	W	G	T	F	N	A	W	I	P	L	F	M	F	K	V	Y	G	F
Secondary structure
SS confidence
Disorder					?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																																									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		N	L	K	E	I	A	M	F	A	W	M	P	M	L	F	A	D	L	G	C	I	L	G	G	Y	L	P	P	L	F	Q	R	W	F	G	V	N	L	I	V	S	R	K	M	V	V	T	L	G	A	V	L	M	I	G	P	G	M	I	G
Secondary structure
SS confidence
Disorder																																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		L	F	T	N	P	Y	V	A	I	M	L	L	C	I	G	G	F	A	H	Q	A	L	S	G	A	L	I	T	L	S	S	D	V	F	G	R	N	E	V	A	T	A	N	G	L	T	G	M	S	A	W	L	A	S	T	L	F	A	L	V
Secondary structure
SS confidence
Disorder																																			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.
Sequence		V	G	A	L	A	D	T	I	G	F	S	P	L	F	A	V	L	A	V	F	D	L	L	G	A	L	V	I	W	T	V	L	Q	N	K	P	A	I	E	V	A	Q	E	T	H	N	D	P	A	P	Q	H
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 1pw4 chain A Region: 28 - 468 Aligned: 426 Modelled: 431 Confidence: 100.0% Identity: 18% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 1pv7 chain A Region: 41 - 469 Aligned: 416 Modelled: 429 Confidence: 100.0% Identity: 12% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 2gfp chain A Region: 51 - 445 Aligned: 370 Modelled: 377 Confidence: 100.0% Identity: 16% PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli Phyre2 PDB 3o7p chain A Region: 45 - 455 Aligned: 394 Modelled: 406 Confidence: 100.0% Identity: 14% PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) Phyre2 PDB 2xut chain C Region: 53 - 451 Aligned: 399 Modelled: 399 Confidence: 100.0% Identity: 11% PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter. Phyre2 PDB 3qnq chain D Region: 418 - 471 Aligned: 54 Modelled: 54 Confidence: 34.6% Identity: 13% PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system Phyre2 PDB 3b60 chain A domain 2 Region: 35 - 115 Aligned: 81 Modelled: 81 Confidence: 22.7% Identity: 9% Fold: ABC transporter transmembrane region Superfamily: ABC transporter transmembrane region Family: ABC transporter transmembrane region Phyre2 PDB 2pkg chain C domain 1 Region: 8 - 25 Aligned: 18 Modelled: 18 Confidence: 18.5% Identity: 33% Fold: T-antigen specific domain-like Superfamily: T-antigen specific domain-like Family: T-antigen specific domain-like Phyre2 PDB 3hd6 chain A Region: 364 - 471 Aligned: 108 Modelled: 108 Confidence: 14.8% Identity: 15% PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg Phyre2 PDB 1pf4 chain A domain 2 Region: 35 - 115 Aligned: 81 Modelled: 81 Confidence: 10.7% Identity: 9% Fold: ABC transporter transmembrane region Superfamily: ABC transporter transmembrane region Family: ABC transporter transmembrane region Phyre2 PDB 3b9y chain A Region: 364 - 471 Aligned: 108 Modelled: 108 Confidence: 10.4% Identity: 17% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein Phyre2 PDB 2knc chain A Region: 430 - 467 Aligned: 38 Modelled: 38 Confidence: 10.1% Identity: 18% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2g9p chain A Region: 104 - 117 Aligned: 14 Modelled: 14 Confidence: 9.6% Identity: 21% PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom Phyre2 PDB 3pro chain C domain 1 Region: 72 - 113 Aligned: 42 Modelled: 42 Confidence: 9.4% Identity: 12% Fold: Alpha-lytic protease prodomain-like Superfamily: Alpha-lytic protease prodomain Family: Alpha-lytic protease prodomain Phyre2 PDB 1fc3 chain A Region: 42 - 87 Aligned: 45 Modelled: 46 Confidence: 7.6% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: Spo0A Phyre2 PDB 1lq1 chain A Region: 42 - 87 Aligned: 45 Modelled: 46 Confidence: 7.1% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: Spo0A Phyre2 PDB 2aj2 chain A Region: 3 - 18 Aligned: 16 Modelled: 16 Confidence: 6.5% Identity: 25% 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. Phyre2 PDB 3arc chain T Region: 435 - 459 Aligned: 25 Modelled: 25 Confidence: 6.0% Identity: 12% PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 3a0b chain T Region: 435 - 459 Aligned: 25 Modelled: 25 Confidence: 6.0% Identity: 12% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 2oar chain A domain 1 Region: 402 - 471 Aligned: 70 Modelled: 70 Confidence: 5.6% Identity: 16% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 1 d1pw4a_ 2 d1pv7a_ 3 c2gfpA_ 4 c3o7pA_ 5 c2xutC_ 6 c3qnqD_ 7 d3b60a2 8 d2pkgc1 9 c3hd6A_ 10 d1pf4a2 11 c3b9yA_ 12 c2kncA_ 13 c2g9pA_ 14 d3proc1 15 d1fc3a_ 16 d1lq1a_ 17 c2aj2A_ 18 c3arct_ 19 c3a0bT_ 20 d2oara1 21 22

Detailed template information

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

1 d1pw4a_ 100.0 18 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 d1pv7a_ 100.0 12 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 3 c2gfpA_ 100.0 16 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli 4 c3o7pA_ 100.0 14 PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) 5 c2xutC_ 100.0 11 PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter. 6 c3qnqD_ 34.6 13 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 7 d3b60a2 22.7 9 Fold:ABC transporter transmembrane region Superfamily:ABC transporter transmembrane region Family:ABC transporter transmembrane region 8 d2pkgc1 18.5 33 Fold:T-antigen specific domain-like Superfamily:T-antigen specific domain-like Family:T-antigen specific domain-like 9 c3hd6A_ 14.8 15 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg 10 d1pf4a2 10.7 9 Fold:ABC transporter transmembrane region Superfamily:ABC transporter transmembrane region Family:ABC transporter transmembrane region 11 c3b9yA_ 10.4 17 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 12 c2kncA_ 10.1 18 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 13 c2g9pA_ 9.6 21 PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom 14 d3proc1 9.4 12 Fold:Alpha-lytic protease prodomain-like Superfamily:Alpha-lytic protease prodomain Family:Alpha-lytic protease prodomain 15 d1fc3a_ 7.6 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:Spo0A 16 d1lq1a_ 7.1 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:Spo0A 17 c2aj2A_ 6.5 25 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. 18 c3arct_ 6.0 12 PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 19 c3a0bT_ 6.0 12 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex 20 d2oara1 5.6 16 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 21 c3shpA_ not modelled 5.5 36 PDB header:transferase Chain: A: PDB Molecule:putative acetyltransferase sthe_0691; PDBTitle: crystal structure of putative acetyltransferase from sphaerobacter2 thermophilus dsm 20745 22 d1fftb2 not modelled 5.2 10 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region

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