Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	T	L	Q	G	W	L	L	P	V	F	M	L	P	M	A	V	Y	A	Q	E	A	T	V	K	E	V	H	D	A	P	A	V	R	G	S	I	I	A	N	M	L	Q	E	H	D	N	P	F	T	L	Y	P	Y	D	T	N	Y	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?							?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?							?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	Y	T	Q	T	S	D	L	N	K	E	A	I	A	S	Y	D	W	A	E	N	A	R	K	D	E	V	K	F	Q	L	S	L	A	F	P	L	W	R	G	I	L	G	P	N	S	V	L	G	A	S	Y	T	Q	K	S	W	W	Q	L
Secondary structure
SS confidence
Disorder											?	?			?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		S	N	S	E	E	S	S	P	F	R	E	T	N	Y	E	P	Q	L	F	L	G	F	A	T	D	Y	R	F	A	G	W	T	L	R	D	V	E	M	G	Y	N	H	D	S	N	G	R	S	D	P	T	S	R	S	W	N	R	L	Y	T
Secondary structure
SS confidence
Disorder							?				?	?																	?		?			?												?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		R	L	M	A	E	N	G	N	W	L	V	E	V	K	P	W	Y	V	V	G	N	T	D	D	N	P	D	I	T	K	Y	M	G	Y	Y	Q	L	K	I	G	Y	H	L	G	D	A	V	L	S	A	K	G	Q	Y	N	W	N	T	G	Y
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.
Sequence		G	G	A	E	L	G	L	S	Y	P	I	T	K	H	V	R	L	Y	T	Q	V	Y	S	G	Y	G	E	S	L	I	D	Y	N	F	N	Q	T	R	V	G	V	G	V	M	L	N	D	L	F
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 1qd6 chain C Region: 50 - 289 Aligned: 240 Modelled: 240 Confidence: 100.0% Identity: 100% PDB header:membrane protein Chain: C: PDB Molecule:protein (outer membrane phospholipase (ompla)); PDBTitle: outer membrane phospholipase a from escherichia coli Phyre2 PDB 1fw3 chain A Region: 48 - 289 Aligned: 241 Modelled: 242 Confidence: 100.0% Identity: 99% PDB header:hydrolase, membrane protein Chain: A: PDB Molecule:outer membrane phospholipase a; PDBTitle: outer membrane phospholipase a from escherichia coli Phyre2 PDB 2iwv chain D Region: 122 - 286 Aligned: 160 Modelled: 165 Confidence: 82.8% Identity: 15% PDB header:ion channel Chain: D: PDB Molecule:outer membrane protein g; PDBTitle: structure of the monomeric outer membrane porin ompg in the2 open and closed conformation Phyre2 PDB 2vve chain B Region: 139 - 232 Aligned: 77 Modelled: 78 Confidence: 50.8% Identity: 26% PDB header:viral protein Chain: B: PDB Molecule:spike protein p1; PDBTitle: crystal structure of the stem and receptor binding domain2 of the spike protein p1 from bacteriophage pm2 Phyre2 PDB 2por chain A Region: 215 - 286 Aligned: 66 Modelled: 72 Confidence: 40.7% Identity: 17% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2w0c chain L Region: 139 - 232 Aligned: 78 Modelled: 79 Confidence: 29.0% Identity: 22% PDB header:virus Chain: L: PDB Molecule:protein 2; PDBTitle: x-ray structure of the entire lipid-containing2 bacteriophage pm2 Phyre2 PDB 2wjq chain A Region: 137 - 286 Aligned: 138 Modelled: 150 Confidence: 19.0% Identity: 16% PDB header:transport protein Chain: A: PDB Molecule:probable n-acetylneuraminic acid outer membrane channel PDBTitle: nanc porin structure in hexagonal crystal form. Phyre2 PDB 2fgq chain X domain 1 Region: 155 - 286 Aligned: 129 Modelled: 132 Confidence: 17.3% Identity: 18% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2vvd chain A Region: 139 - 232 Aligned: 78 Modelled: 77 Confidence: 14.7% Identity: 22% PDB header:viral protein Chain: A: PDB Molecule:spike protein p1; PDBTitle: crystal structure of the receptor binding domain of the2 spike protein p1 from bacteriophage pm2 Phyre2 PDB 1xrs chain B domain 2 Region: 88 - 97 Aligned: 10 Modelled: 10 Confidence: 14.2% Identity: 60% 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 Phyre2 PDB 2kz3 chain A Region: 1 - 43 Aligned: 43 Modelled: 43 Confidence: 13.6% Identity: 21% PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein rad51l3; PDBTitle: backbone 1h, 13c, and 15n chemical shift assignments for human rad51d2 from 1 to 83 Phyre2 PDB 1wpu chain A domain 1 Region: 265 - 284 Aligned: 20 Modelled: 20 Confidence: 8.8% Identity: 25% Fold: Hut operon positive regulatory protein HutP Superfamily: Hut operon positive regulatory protein HutP Family: Hut operon positive regulatory protein HutP Phyre2 PDB 1w0n chain A Region: 121 - 129 Aligned: 9 Modelled: 9 Confidence: 8.8% Identity: 33% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Family 36 carbohydrate binding module, CBM36 Phyre2 PDB 3bux chain B domain 3 Region: 196 - 209 Aligned: 14 Modelled: 14 Confidence: 8.0% Identity: 36% Fold: SH2-like Superfamily: SH2 domain Family: SH2 domain Phyre2 PDB 1ais chain A domain 1 Region: 129 - 139 Aligned: 11 Modelled: 11 Confidence: 7.1% Identity: 27% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1mp9 chain A domain 1 Region: 129 - 139 Aligned: 11 Modelled: 11 Confidence: 6.7% Identity: 27% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 2w56 chain B Region: 129 - 167 Aligned: 27 Modelled: 39 Confidence: 6.5% Identity: 30% PDB header:unknown function Chain: B: PDB Molecule:vc0508; PDBTitle: structure of the hypothetical protein vc0508 from vibrio cholerae2 vsp-ii pathogenicity island Phyre2 PDB 1pg5 chain A domain 1 Region: 254 - 271 Aligned: 18 Modelled: 18 Confidence: 6.1% Identity: 33% Fold: ATC-like Superfamily: Aspartate/ornithine carbamoyltransferase Family: Aspartate/ornithine carbamoyltransferase Phyre2 PDB 1uwk chain A Region: 123 - 136 Aligned: 14 Modelled: 14 Confidence: 6.0% Identity: 36% Fold: Urocanase Superfamily: Urocanase Family: Urocanase Phyre2 PDB 3al0 chain B Region: 264 - 274 Aligned: 11 Modelled: 11 Confidence: 6.0% Identity: 36% PDB header:ligase/rna Chain: B: PDB Molecule:aspartyl/glutamyl-trna(asn/gln) amidotransferase subunit b; PDBTitle: crystal structure of the glutamine transamidosome from thermotoga2 maritima in the glutamylation state. Phyre2 1 c1qd6C_ 2 c1fw3A_ 3 c2iwvD_ 4 c2vveB_ 5 d2pora_ 6 c2w0cL_ 7 c2wjqA_ 8 d2fgqx1 9 c2vvdA_ 10 d1xrsb2 11 c2kz3A_ 12 d1wpua1 13 d1w0na_ 14 d3buxb3 15 d1aisa1 16 d1mp9a1 17 c2w56B_ 18 d1pg5a1 19 d1uwka_ 20 c3al0B_ 21 22 23 24 25

Detailed template information

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

1 c1qd6C_ 100.0 100 PDB header:membrane protein Chain: C: PDB Molecule:protein (outer membrane phospholipase (ompla)); PDBTitle: outer membrane phospholipase a from escherichia coli 2 c1fw3A_ 100.0 99 PDB header:hydrolase, membrane protein Chain: A: PDB Molecule:outer membrane phospholipase a; PDBTitle: outer membrane phospholipase a from escherichia coli 3 c2iwvD_ 82.8 15 PDB header:ion channel Chain: D: PDB Molecule:outer membrane protein g; PDBTitle: structure of the monomeric outer membrane porin ompg in the2 open and closed conformation 4 c2vveB_ 50.8 26 PDB header:viral protein Chain: B: PDB Molecule:spike protein p1; PDBTitle: crystal structure of the stem and receptor binding domain2 of the spike protein p1 from bacteriophage pm2 5 d2pora_ 40.7 17 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 6 c2w0cL_ 29.0 22 PDB header:virus Chain: L: PDB Molecule:protein 2; PDBTitle: x-ray structure of the entire lipid-containing2 bacteriophage pm2 7 c2wjqA_ 19.0 16 PDB header:transport protein Chain: A: PDB Molecule:probable n-acetylneuraminic acid outer membrane channel PDBTitle: nanc porin structure in hexagonal crystal form. 8 d2fgqx1 17.3 18 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 9 c2vvdA_ 14.7 22 PDB header:viral protein Chain: A: PDB Molecule:spike protein p1; PDBTitle: crystal structure of the receptor binding domain of the2 spike protein p1 from bacteriophage pm2 10 d1xrsb2 14.2 60 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 11 c2kz3A_ 13.6 21 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein rad51l3; PDBTitle: backbone 1h, 13c, and 15n chemical shift assignments for human rad51d2 from 1 to 83 12 d1wpua1 8.8 25 Fold:Hut operon positive regulatory protein HutP Superfamily:Hut operon positive regulatory protein HutP Family:Hut operon positive regulatory protein HutP 13 d1w0na_ 8.8 33 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Family 36 carbohydrate binding module, CBM36 14 d3buxb3 8.0 36 Fold:SH2-like Superfamily:SH2 domain Family:SH2 domain 15 d1aisa1 7.1 27 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 16 d1mp9a1 6.7 27 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 17 c2w56B_ 6.5 30 PDB header:unknown function Chain: B: PDB Molecule:vc0508; PDBTitle: structure of the hypothetical protein vc0508 from vibrio cholerae2 vsp-ii pathogenicity island 18 d1pg5a1 6.1 33 Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase 19 d1uwka_ 6.0 36 Fold:Urocanase Superfamily:Urocanase Family:Urocanase 20 c3al0B_ 6.0 36 PDB header:ligase/rna Chain: B: PDB Molecule:aspartyl/glutamyl-trna(asn/gln) amidotransferase subunit b; PDBTitle: crystal structure of the glutamine transamidosome from thermotoga2 maritima in the glutamylation state. 21 c3btpB_ not modelled 5.9 67 PDB header:dna binding protein, chaperone Chain: B: PDB Molecule:protein vire1; PDBTitle: crystal structure of agrobacterium tumefaciens vire2 in complex with2 its chaperone vire1: a novel fold and implications for dna binding 22 d2ogqa1 not modelled 5.6 31 Fold:Polo-box domain Superfamily:Polo-box domain Family:Polo-box duplicated region 23 d2zfga1 not modelled 5.4 18 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 24 c2fknC_ not modelled 5.4 50 PDB header:lyase Chain: C: PDB Molecule:urocanate hydratase; PDBTitle: crystal structure of urocanase from bacillus subtilis 25 c1pg5A_ not modelled 5.2 35 PDB header:transferase Chain: A: PDB Molecule:aspartate carbamoyltransferase; PDBTitle: crystal structure of the unligated (t-state) aspartate2 transcarbamoylase from the extremely thermophilic archaeon sulfolobus3 acidocaldarius

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