Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	K	L	L	P	I	L	I	G	L	S	L	S	G	F	S	S	L	S	Q	A	E	N	L	M	Q	V	Y	Q	Q	A	R	L	S	N	P	E	L	R	K	S	A	A	D	R	D	A	A	F	E	K	I	N	E	A	R	S	P	L
Secondary structure
SS confidence
Disorder		?	?	?											?	?	?	?	?	?	?	?																																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	P	Q	L	G	L	G	A	D	Y	T	Y	S	N	G	Y	R	D	A	N	G	I	N	S	N	A	T	S	A	S	L	Q	L	T	Q	S	I	F	D	M	S	K	W	R	A	L	T	L	Q	E	K	A	A	G	I	Q	D	V	T	Y
Secondary structure
SS confidence
Disorder												?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Q	T	D	Q	Q	T	L	I	L	N	T	A	T	A	Y	F	N	V	L	N	A	I	D	V	L	S	Y	T	Q	A	Q	K	E	A	I	Y	R	Q	L	D	Q	T	T	Q	R	F	N	V	G	L	V	A	I	T	D	V	Q	N	A	R
Secondary structure
SS confidence
Disorder																																																	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	Q	Y	D	T	V	L	A	N	E	V	T	A	R	N	N	L	D	N	A	V	E	Q	L	R	Q	I	T	G	N	Y	Y	P	E	L	A	A	L	N	V	E	N	F	K	T	D	K	P	Q	P	V	N	A	L	L	K	E	A	E	K
Secondary structure
SS confidence
Disorder																																		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		R	N	L	S	L	L	Q	A	R	L	S	Q	D	L	A	R	E	Q	I	R	Q	A	Q	D	G	H	L	P	T	L	D	L	T	A	S	T	G	I	S	D	T	S	Y	S	G	S	K	T	R	G	A	A	G	T	Q	Y	D	D	S	N
Secondary structure
SS confidence
Disorder		?																						?	?	?													?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		M	G	Q	N	K	V	G	L	S	F	S	L	P	I	Y	Q	G	G	M	V	N	S	Q	V	K	Q	A	Q	Y	N	F	V	G	A	S	E	Q	L	E	S	A	H	R	S	V	V	Q	T	V	R	S	S	F	N	N	I	N	A	S	I
Secondary structure
SS confidence
Disorder		?	?	?																	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		S	S	I	N	A	Y	K	Q	A	V	V	S	A	Q	S	S	L	D	A	M	E	A	G	Y	S	V	G	T	R	T	I	V	D	V	L	D	A	T	T	T	L	Y	N	A	K	Q	E	L	A	N	A	R	Y	N	Y	L	I	N	Q	L
Secondary structure
SS confidence
Disorder																													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		N	I	K	S	A	L	G	T	L	N	E	Q	D	L	L	A	L	N	N	A	L	S	K	P	V	S	T	N	P	E	N	V	A	P	Q	T	P	E	Q	N	A	I	A	D	G	Y	A	P	D	S	P	A	P	V	V	Q	Q	T	S	A
Secondary structure
SS confidence
Disorder																		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?			?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.
Sequence		R	T	T	T	S	N	G	H	N	P	F	R	N
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 1tqq chain C Region: 23 - 450 Aligned: 428 Modelled: 428 Confidence: 100.0% Identity: 100% 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: 23 - 449 Aligned: 427 Modelled: 427 Confidence: 100.0% Identity: 99% 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 - 427 Aligned: 393 Modelled: 404 Confidence: 100.0% Identity: 17% PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusc; PDBTitle: outer membrane protein cusc Phyre2 PDB 1wp1 chain A Region: 24 - 433 Aligned: 400 Modelled: 410 Confidence: 100.0% Identity: 21% Fold: Outer membrane efflux proteins (OEP) Superfamily: Outer membrane efflux proteins (OEP) Family: Outer membrane efflux proteins (OEP) Phyre2 PDB 1yc9 chain A Region: 24 - 431 Aligned: 392 Modelled: 408 Confidence: 100.0% Identity: 20% 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 2v7s chain A Region: 235 - 331 Aligned: 97 Modelled: 97 Confidence: 51.5% Identity: 10% PDB header:unknown function Chain: A: PDB Molecule:probable conserved lipoprotein lppa; PDBTitle: crystal structure of the putative lipoprotein lppa from2 mycobacterium tuberculosis Phyre2 PDB 3fpp chain B Region: 343 - 425 Aligned: 83 Modelled: 83 Confidence: 37.6% Identity: 8% PDB header:membrane protein Chain: B: PDB Molecule:macrolide-specific efflux protein maca; PDBTitle: crystal structure of e.coli maca Phyre2 PDB 2l06 chain A Region: 157 - 212 Aligned: 56 Modelled: 56 Confidence: 26.3% Identity: 11% 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 PDB 3ohw chain B Region: 156 - 212 Aligned: 57 Modelled: 57 Confidence: 23.8% Identity: 4% 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 Phyre2 PDB 2ky4 chain A Region: 156 - 212 Aligned: 57 Modelled: 57 Confidence: 21.2% Identity: 9% 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 Phyre2 PDB 2l3w chain A Region: 159 - 212 Aligned: 54 Modelled: 54 Confidence: 20.1% Identity: 11% 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 Phyre2 PDB 3pru chain D Region: 162 - 212 Aligned: 51 Modelled: 51 Confidence: 18.9% Identity: 6% 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 Phyre2 PDB 3sog chain A Region: 313 - 427 Aligned: 113 Modelled: 115 Confidence: 17.1% Identity: 7% PDB header:structural protein Chain: A: PDB Molecule:amphiphysin; PDBTitle: crystal structure of the bar domain of human amphiphysin, isoform 1 Phyre2 PDB 1urq chain C Region: 142 - 207 Aligned: 66 Modelled: 66 Confidence: 11.7% Identity: 14% 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 2z0v chain A Region: 343 - 426 Aligned: 81 Modelled: 84 Confidence: 11.3% Identity: 10% PDB header:endocytosis Chain: A: PDB Molecule:sh3-containing grb2-like protein 3; PDBTitle: crystal structure of bar domain of endophilin-iii Phyre2 PDB 2f1m chain A Region: 350 - 422 Aligned: 73 Modelled: 73 Confidence: 9.2% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:acriflavine resistance protein a; PDBTitle: conformational flexibility in the multidrug efflux system protein acra Phyre2 PDB 3b5n chain C Region: 147 - 207 Aligned: 61 Modelled: 61 Confidence: 7.8% Identity: 13% PDB header:membrane protein Chain: C: PDB Molecule:protein transport protein sec9; PDBTitle: structure of the yeast plasma membrane snare complex Phyre2 PDB 1nhl chain A Region: 156 - 207 Aligned: 52 Modelled: 52 Confidence: 5.4% Identity: 13% PDB header:protein transport Chain: A: PDB Molecule:synaptosomal-associated protein 23; PDBTitle: snap-23n structure Phyre2 1 c1tqqC_ 2 d1ek9a_ 3 c3pikA_ 4 d1wp1a_ 5 c1yc9A_ 6 c2v7sA_ 7 c3fppB_ 8 c2l06A_ 9 c3ohwB_ 10 c2ky4A_ 11 c2l3wA_ 12 c3pruD_ 13 c3sogA_ 14 c1urqC_ 15 c2z0vA_ 16 c2f1mA_ 17 c3b5nC_ 18 c1nhlA_

Detailed template information

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

1 c1tqqC_ 100.0 100 PDB header:transport protein Chain: C: PDB Molecule:outer membrane protein tolc; PDBTitle: structure of tolc in complex with hexamminecobalt 2 d1ek9a_ 100.0 99 Fold:Outer membrane efflux proteins (OEP) Superfamily:Outer membrane efflux proteins (OEP) Family:Outer membrane efflux proteins (OEP) 3 c3pikA_ 100.0 17 PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusc; PDBTitle: outer membrane protein cusc 4 d1wp1a_ 100.0 21 Fold:Outer membrane efflux proteins (OEP) Superfamily:Outer membrane efflux proteins (OEP) Family:Outer membrane efflux proteins (OEP) 5 c1yc9A_ 100.0 20 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 6 c2v7sA_ 51.5 10 PDB header:unknown function Chain: A: PDB Molecule:probable conserved lipoprotein lppa; PDBTitle: crystal structure of the putative lipoprotein lppa from2 mycobacterium tuberculosis 7 c3fppB_ 37.6 8 PDB header:membrane protein Chain: B: PDB Molecule:macrolide-specific efflux protein maca; PDBTitle: crystal structure of e.coli maca 8 c2l06A_ 26.3 11 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 9 c3ohwB_ 23.8 4 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 10 c2ky4A_ 21.2 9 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 11 c2l3wA_ 20.1 11 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 12 c3pruD_ 18.9 6 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 13 c3sogA_ 17.1 7 PDB header:structural protein Chain: A: PDB Molecule:amphiphysin; PDBTitle: crystal structure of the bar domain of human amphiphysin, isoform 1 14 c1urqC_ 11.7 14 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 15 c2z0vA_ 11.3 10 PDB header:endocytosis Chain: A: PDB Molecule:sh3-containing grb2-like protein 3; PDBTitle: crystal structure of bar domain of endophilin-iii 16 c2f1mA_ 9.2 10 PDB header:transport protein Chain: A: PDB Molecule:acriflavine resistance protein a; PDBTitle: conformational flexibility in the multidrug efflux system protein acra 17 c3b5nC_ 7.8 13 PDB header:membrane protein Chain: C: PDB Molecule:protein transport protein sec9; PDBTitle: structure of the yeast plasma membrane snare complex 18 c1nhlA_ 5.4 13 PDB header:protein transport Chain: A: PDB Molecule:synaptosomal-associated protein 23; PDBTitle: snap-23n structure

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