Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	N	R	Q	L	S	R	L	L	L	C	S	I	L	G	S	T	T	L	I	S	G	C	A	L	V	R	K	D	S	A	P	H	Q	Q	L	K	P	E	Q	I	K	L	A	D	D	I	H	L	A	S	S	G	W	P	Q	A	Q	W
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																	?	?							?	?			?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		W	K	Q	L	N	D	P	Q	L	D	A	L	I	Q	R	T	L	S	G	S	H	T	L	A	E	A	K	L	R	E	E	K	A	Q	S	Q	A	D	L	L	D	A	G	S	Q	L	Q	V	A	A	L	G	M	L	N	R	Q	R	V	S
Secondary structure
SS confidence
Disorder																																										?	?	?							?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	N	G	F	L	S	P	Y	S	M	D	A	P	A	L	G	M	D	G	P	Y	Y	T	E	A	T	V	G	L	F	A	G	L	D	L	D	L	W	G	V	H	R	S	A	V	A	A	A	I	G	A	H	N	A	A	L	A	E	T	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	V	E	L	S	L	A	T	G	V	A	Q	L	Y	Y	S	M	Q	A	S	Y	Q	M	L	D	L	L	E	Q	T	H	D	V	I	D	Y	A	V	K	A	H	Q	S	K	V	A	H	G	L	E	A	Q	V	P	F	H	G	A	R	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		Q	I	L	A	V	D	K	Q	I	V	A	V	K	G	Q	I	T	E	T	R	E	S	L	R	A	L	I	G	A	G	A	S	D	M	P	E	I	R	P	V	A	L	P	Q	V	Q	T	G	I	P	A	T	L	S	Y	E	L	L	A	R
Secondary structure
SS confidence
Disorder																																	?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		R	P	D	L	Q	A	M	R	W	Y	V	Q	A	S	L	D	Q	V	D	S	A	R	A	L	F	Y	P	S	F	D	I	K	A	F	F	G	L	D	S	I	H	L	H	T	L	F	K	K	T	S	R	Q	F	N	F	I	P	G	L	K
Secondary structure
SS confidence
Disorder																																	?	?	?	?	?	?	?		?	?	?	?	?	?							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		L	P	L	F	D	G	G	R	L	N	A	N	L	E	G	T	R	A	A	S	N	M	M	I	E	R	Y	N	Q	S	V	L	N	A	V	R	D	V	A	V	N	G	T	R	L	Q	T	L	N	D	E	R	E	M	Q	A	E	R	V	E
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		A	T	R	F	T	Q	R	A	A	E	A	A	Y	Q	R	G	L	T	S	R	L	Q	A	T	E	A	R	L	P	V	L	A	E	E	M	S	L	L	M	L	D	S	R	R	V	I	Q	S	I	Q	L	M	K	S	L	G	G	G	Y	Q
Secondary structure
SS confidence
Disorder																																																													?
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		A	G	P	V	V	E	K	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 1wp1 chain A Region: 24 - 485 Aligned: 453 Modelled: 462 Confidence: 100.0% Identity: 22% Fold: Outer membrane efflux proteins (OEP) Superfamily: Outer membrane efflux proteins (OEP) Family: Outer membrane efflux proteins (OEP) Phyre2 PDB 3pik chain A Region: 24 - 478 Aligned: 429 Modelled: 440 Confidence: 100.0% Identity: 27% PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusc; PDBTitle: outer membrane protein cusc Phyre2 PDB 1yc9 chain A Region: 55 - 480 Aligned: 411 Modelled: 426 Confidence: 100.0% Identity: 28% PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein; PDBTitle: the crystal structure of the outer membrane protein vcec from the2 bacterial pathogen vibrio cholerae at 1.8 resolution Phyre2 PDB 1tqq chain C Region: 68 - 476 Aligned: 394 Modelled: 395 Confidence: 100.0% Identity: 14% PDB header:transport protein Chain: C: PDB Molecule:outer membrane protein tolc; PDBTitle: structure of tolc in complex with hexamminecobalt Phyre2 PDB 1ek9 chain A Region: 68 - 476 Aligned: 394 Modelled: 392 Confidence: 100.0% Identity: 14% Fold: Outer membrane efflux proteins (OEP) Superfamily: Outer membrane efflux proteins (OEP) Family: Outer membrane efflux proteins (OEP) Phyre2 PDB 3fpp chain B Region: 185 - 266 Aligned: 82 Modelled: 82 Confidence: 47.9% Identity: 12% PDB header:membrane protein Chain: B: PDB Molecule:macrolide-specific efflux protein maca; PDBTitle: crystal structure of e.coli maca Phyre2 PDB 1urq chain C Region: 201 - 266 Aligned: 66 Modelled: 66 Confidence: 28.1% Identity: 12% PDB header:transport protein Chain: C: PDB Molecule:synaptosomal-associated protein 25; PDBTitle: crystal structure of neuronal q-snares in complex with2 r-snare motif of tomosyn Phyre2 PDB 2ijr chain A domain 1 Region: 16 - 66 Aligned: 51 Modelled: 51 Confidence: 27.7% Identity: 14% Fold: Api92-like Superfamily: Api92-like Family: Api92-like Phyre2 PDB 3sog chain A Region: 362 - 476 Aligned: 113 Modelled: 115 Confidence: 22.3% Identity: 10% PDB header:structural protein Chain: A: PDB Molecule:amphiphysin; PDBTitle: crystal structure of the bar domain of human amphiphysin, isoform 1 Phyre2 PDB 2zro chain A Region: 470 - 486 Aligned: 17 Modelled: 17 Confidence: 19.0% Identity: 47% PDB header:hydrolase Chain: A: PDB Molecule:protein reca; PDBTitle: msreca adp form iv Phyre2 PDB 1mo6 chain A domain 1 Region: 470 - 486 Aligned: 17 Modelled: 17 Confidence: 14.9% Identity: 47% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: RecA protein-like (ATPase-domain) Phyre2 PDB 3b5n chain C Region: 206 - 266 Aligned: 61 Modelled: 61 Confidence: 14.7% Identity: 15% PDB header:membrane protein Chain: C: PDB Molecule:protein transport protein sec9; PDBTitle: structure of the yeast plasma membrane snare complex Phyre2 PDB 1v5r chain A domain 1 Region: 475 - 480 Aligned: 6 Modelled: 6 Confidence: 14.7% Identity: 50% Fold: N domain of copper amine oxidase-like Superfamily: GAS2 domain-like Family: GAS2 domain Phyre2 PDB 1xp8 chain A domain 1 Region: 470 - 486 Aligned: 17 Modelled: 17 Confidence: 14.4% Identity: 41% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: RecA protein-like (ATPase-domain) Phyre2 PDB 1xp8 chain A Region: 470 - 486 Aligned: 17 Modelled: 17 Confidence: 13.8% Identity: 41% PDB header:dna binding protein Chain: A: PDB Molecule:reca protein; PDBTitle: "deinococcus radiodurans reca in complex with atp-gamma-s" Phyre2 PDB 1ube chain A domain 1 Region: 470 - 486 Aligned: 17 Modelled: 17 Confidence: 13.3% Identity: 47% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: RecA protein-like (ATPase-domain) Phyre2 PDB 2rec chain B Region: 470 - 486 Aligned: 17 Modelled: 17 Confidence: 12.0% Identity: 47% PDB header:helicase PDB COMPND: Phyre2 PDB 2vdf chain A domain 1 Region: 474 - 486 Aligned: 13 Modelled: 13 Confidence: 9.8% Identity: 38% Fold: Transmembrane beta-barrels Superfamily: OMPT-like Family: Outer membrane adhesin/invasin OpcA Phyre2 PDB 1l4a chain C Region: 199 - 263 Aligned: 65 Modelled: 65 Confidence: 8.1% Identity: 8% PDB header:endocytosis/exocytosis Chain: C: PDB Molecule:s-snap25 fusion protein; PDBTitle: x-ray structure of the neuronal complexin/snare complex2 from the squid loligo pealei Phyre2 PDB 2l06 chain A Region: 216 - 271 Aligned: 56 Modelled: 56 Confidence: 8.0% Identity: 18% PDB header:protein binding Chain: A: PDB Molecule:phycobilisome lcm core-membrane linker polypeptide; PDBTitle: solution nmr structure of the pbs linker polypeptide domain (fragment2 254-400) of phycobilisome linker protein apce from synechocystis sp.3 pcc 6803. northeast structural genomics consortium target sgr209c Phyre2 1 d1wp1a_ 2 c3pikA_ 3 c1yc9A_ 4 c1tqqC_ 5 d1ek9a_ 6 c3fppB_ 7 c1urqC_ 8 d2ijra1 9 c3sogA_ 10 c2zroA_ 11 d1mo6a1 12 c3b5nC_ 13 d1v5ra1 14 d1xp8a1 15 c1xp8A_ 16 d1ubea1 17 c2recB_ 18 d2vdfa1 19 c1l4aC_ 20 c2l06A_ 21 22 23 24 25 26 27 28 29

Detailed template information

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

1 d1wp1a_ 100.0 22 Fold:Outer membrane efflux proteins (OEP) Superfamily:Outer membrane efflux proteins (OEP) Family:Outer membrane efflux proteins (OEP) 2 c3pikA_ 100.0 27 PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusc; PDBTitle: outer membrane protein cusc 3 c1yc9A_ 100.0 28 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein; PDBTitle: the crystal structure of the outer membrane protein vcec from the2 bacterial pathogen vibrio cholerae at 1.8 resolution 4 c1tqqC_ 100.0 14 PDB header:transport protein Chain: C: PDB Molecule:outer membrane protein tolc; PDBTitle: structure of tolc in complex with hexamminecobalt 5 d1ek9a_ 100.0 14 Fold:Outer membrane efflux proteins (OEP) Superfamily:Outer membrane efflux proteins (OEP) Family:Outer membrane efflux proteins (OEP) 6 c3fppB_ 47.9 12 PDB header:membrane protein Chain: B: PDB Molecule:macrolide-specific efflux protein maca; PDBTitle: crystal structure of e.coli maca 7 c1urqC_ 28.1 12 PDB header:transport protein Chain: C: PDB Molecule:synaptosomal-associated protein 25; PDBTitle: crystal structure of neuronal q-snares in complex with2 r-snare motif of tomosyn 8 d2ijra1 27.7 14 Fold:Api92-like Superfamily:Api92-like Family:Api92-like 9 c3sogA_ 22.3 10 PDB header:structural protein Chain: A: PDB Molecule:amphiphysin; PDBTitle: crystal structure of the bar domain of human amphiphysin, isoform 1 10 c2zroA_ 19.0 47 PDB header:hydrolase Chain: A: PDB Molecule:protein reca; PDBTitle: msreca adp form iv 11 d1mo6a1 14.9 47 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain) 12 c3b5nC_ 14.7 15 PDB header:membrane protein Chain: C: PDB Molecule:protein transport protein sec9; PDBTitle: structure of the yeast plasma membrane snare complex 13 d1v5ra1 14.7 50 Fold:N domain of copper amine oxidase-like Superfamily:GAS2 domain-like Family:GAS2 domain 14 d1xp8a1 14.4 41 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain) 15 c1xp8A_ 13.8 41 PDB header:dna binding protein Chain: A: PDB Molecule:reca protein; PDBTitle: "deinococcus radiodurans reca in complex with atp-gamma-s" 16 d1ubea1 13.3 47 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain) 17 c2recB_ 12.0 47 PDB header:helicase PDB COMPND: 18 d2vdfa1 9.8 38 Fold:Transmembrane beta-barrels Superfamily:OMPT-like Family:Outer membrane adhesin/invasin OpcA 19 c1l4aC_ 8.1 8 PDB header:endocytosis/exocytosis Chain: C: PDB Molecule:s-snap25 fusion protein; PDBTitle: x-ray structure of the neuronal complexin/snare complex2 from the squid loligo pealei 20 c2l06A_ 8.0 18 PDB header:protein binding Chain: A: PDB Molecule:phycobilisome lcm core-membrane linker polypeptide; PDBTitle: solution nmr structure of the pbs linker polypeptide domain (fragment2 254-400) of phycobilisome linker protein apce from synechocystis sp.3 pcc 6803. northeast structural genomics consortium target sgr209c 21 c3ohwB_ not modelled 7.3 12 PDB header:protein binding Chain: B: PDB Molecule:phycobilisome lcm core-membrane linker polypeptide; PDBTitle: x-ray structure of phycobilisome lcm core-membrane linker polypeptide2 (fragment 721-860) from synechocystis sp. pcc 6803, northeast3 structural genomics consortium target sgr209e 22 c3hr8A_ not modelled 7.2 41 PDB header:recombination Chain: A: PDB Molecule:protein reca; PDBTitle: crystal structure of thermotoga maritima reca 23 c2f1mA_ not modelled 6.8 8 PDB header:transport protein Chain: A: PDB Molecule:acriflavine resistance protein a; PDBTitle: conformational flexibility in the multidrug efflux system protein acra 24 c2ky4A_ not modelled 6.7 11 PDB header:photosynthesis Chain: A: PDB Molecule:phycobilisome linker polypeptide; PDBTitle: solution nmr structure of the pbs linker domain of phycobilisome2 linker polypeptide from anabaena sp. northeast structural genomics3 consortium target nsr123e 25 c2l3wA_ not modelled 6.6 14 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 26 c3pruD_ not modelled 6.5 16 PDB header:photosynthesis Chain: D: PDB Molecule:phycobilisome 32.1 kda linker polypeptide, phycocyanin- PDBTitle: crystal structure of phycobilisome 32.1 kda linker polypeptide,2 phycocyanin-associated, rod 1 (fragment 14-158) from synechocystis3 sp. pcc 6803, northeast structural genomics consortium target sgr182a 27 c3brzA_ not modelled 6.5 11 PDB header:transport protein Chain: A: PDB Molecule:todx; PDBTitle: crystal structure of the pseudomonas putida toluene2 transporter todx 28 c1nhlA_ not modelled 6.3 12 PDB header:protein transport Chain: A: PDB Molecule:synaptosomal-associated protein 23; PDBTitle: snap-23n structure 29 c3zqbB_ not modelled 5.9 11 PDB header:cell invasion Chain: B: PDB Molecule:protein prgi, cell invasion protein sipd; PDBTitle: prgi-sipd from salmonella typhimurium

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