Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	M	P	Q	S	L	P	D	T	T	T	P	K	R	R	F	R	W	P	T	G	M	P	Q	L	V	A	L	L	L	V	L	L	V	D	S	L	V	A	P	H	F	W	Q	V	V	L	Q	D	G	R	L	F	G	S	P	I	D	I	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?					?	?	?																												?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	R	A	A	P	V	A	L	L	A	I	G	M	T	L	V	I	A	T	G	G	I	D	L	S	V	G	A	V	M	A	I	A	G	A	T	T	A	A	M	T	V	A	G	F	S	L	P	I	V	L	L	S	A	L	G	T	G	I	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	G	L	W	N	G	I	L	V	A	I	L	K	I	Q	P	F	V	A	T	L	I	L	M	V	A	G	R	G	V	A	Q	L	I	T	A	G	Q	I	V	T	F	N	S	P	D	L	S	W	F	G	S	G	S	L	L	F	L	P	T
Secondary structure
SS confidence
Disorder																																							?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		P	V	I	I	A	V	L	T	L	I	L	F	W	L	L	T	R	K	T	A	L	G	M	F	I	E	A	V	G	I	N	I	R	A	A	K	N	A	G	V	N	T	R	I	I	V	M	L	T	Y	V	L	S	G	L	C	A	A	I	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		G	I	I	V	A	A	D	I	R	G	A	D	A	N	N	A	G	L	W	L	E	L	D	A	I	L	A	V	V	I	G	G	G	S	L	M	G	G	R	F	N	L	L	L	S	V	V	G	A	L	I	I	Q	G	M	N	T	G	I	L
Secondary structure
SS confidence
Disorder									?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.
Sequence		L	S	G	F	P	P	E	M	N	Q	V	V	K	A	V	V	V	L	C	V	L	I	V	Q	S	Q	R	F	I	S	L	I	K	G	V	R	S	R	D	K	T
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 1l7v chain A Region: 9 - 325 Aligned: 301 Modelled: 304 Confidence: 97.9% Identity: 13% Fold: ABC transporter involved in vitamin B12 uptake, BtuC Superfamily: ABC transporter involved in vitamin B12 uptake, BtuC Family: ABC transporter involved in vitamin B12 uptake, BtuC Phyre2 PDB 2nq2 chain A Region: 18 - 324 Aligned: 294 Modelled: 299 Confidence: 96.8% Identity: 17% PDB header:metal transport Chain: A: PDB Molecule:hypothetical abc transporter permease protein PDBTitle: an inward-facing conformation of a putative metal-chelate2 type abc transporter. Phyre2 PDB 3b9y chain A Region: 10 - 135 Aligned: 126 Modelled: 126 Confidence: 49.9% Identity: 14% 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 2b2h chain A Region: 9 - 225 Aligned: 207 Modelled: 217 Confidence: 36.3% Identity: 13% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 3pxp chain A Region: 196 - 228 Aligned: 33 Modelled: 32 Confidence: 15.8% Identity: 18% PDB header:transcription regulator Chain: A: PDB Molecule:helix-turn-helix domain protein; PDBTitle: crystal structure of a pas and dna binding domain containing protein2 (caur_2278) from chloroflexus aurantiacus j-10-fl at 2.30 a3 resolution Phyre2 PDB 2e74 chain G domain 1 Region: 231 - 254 Aligned: 24 Modelled: 24 Confidence: 11.6% Identity: 29% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 4a18 chain U Region: 204 - 223 Aligned: 20 Modelled: 20 Confidence: 9.6% Identity: 25% PDB header:ribosome Chain: U: PDB Molecule:rpl13; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of molecule 1 Phyre2 PDB 3u5e chain L Region: 204 - 223 Aligned: 20 Modelled: 20 Confidence: 9.3% Identity: 20% PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution Phyre2 PDB 1etf chain B Region: 324 - 341 Aligned: 18 Modelled: 18 Confidence: 6.2% Identity: 17% PDB header:viral protein/rna Chain: B: PDB Molecule:rev peptide; PDBTitle: rev response element (rre) rna complexed with rev peptide,2 nmr, minimized average structure Phyre2 PDB 1etg chain B Region: 324 - 341 Aligned: 18 Modelled: 18 Confidence: 6.2% Identity: 17% PDB header:viral protein/rna Chain: B: PDB Molecule:rev peptide; PDBTitle: rev response element (rre) rna complexed with rev peptide,2 nmr, 19 structures Phyre2 1 d1l7va_ 2 c2nq2A_ 3 c3b9yA_ 4 c2b2hA_ 5 c3pxpA_ 6 d2e74g1 7 c4a18U_ 8 c3u5eL_ 9 c1etfB_ 10 c1etgB_

Detailed template information

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

1 d1l7va_ 97.9 13 Fold:ABC transporter involved in vitamin B12 uptake, BtuC Superfamily:ABC transporter involved in vitamin B12 uptake, BtuC Family:ABC transporter involved in vitamin B12 uptake, BtuC 2 c2nq2A_ 96.8 17 PDB header:metal transport Chain: A: PDB Molecule:hypothetical abc transporter permease protein PDBTitle: an inward-facing conformation of a putative metal-chelate2 type abc transporter. 3 c3b9yA_ 49.9 14 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 4 c2b2hA_ 36.3 13 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 5 c3pxpA_ 15.8 18 PDB header:transcription regulator Chain: A: PDB Molecule:helix-turn-helix domain protein; PDBTitle: crystal structure of a pas and dna binding domain containing protein2 (caur_2278) from chloroflexus aurantiacus j-10-fl at 2.30 a3 resolution 6 d2e74g1 11.6 29 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 7 c4a18U_ 9.6 25 PDB header:ribosome Chain: U: PDB Molecule:rpl13; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of molecule 1 8 c3u5eL_ 9.3 20 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 9 c1etfB_ 6.2 17 PDB header:viral protein/rna Chain: B: PDB Molecule:rev peptide; PDBTitle: rev response element (rre) rna complexed with rev peptide,2 nmr, minimized average structure 10 c1etgB_ 6.2 17 PDB header:viral protein/rna Chain: B: PDB Molecule:rev peptide; PDBTitle: rev response element (rre) rna complexed with rev peptide,2 nmr, 19 structures

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