Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	E	Q	F	L	Y	F	L	Q	Q	M	F	N	G	V	T	L	G	S	T	Y	A	L	I	A	I	G	Y	T	M	V	Y	G	I	I	G	M	I	N	F	A	H	G	E	V	Y	M	I	G	S	Y	V	S	F	M	I	I	A	A
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	M	M	M	G	I	D	T	G	W	L	L	V	A	A	G	F	V	G	A	I	V	I	A	S	A	Y	G	W	S	I	E	R	V	A	Y	R	P	V	R	N	S	K	R	L	I	A	L	I	S	A	I	G	M	S	I	F	L	Q	N
Secondary structure
SS confidence
Disorder				?		?																																							?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Y	V	S	L	T	E	G	S	R	D	V	A	L	P	S	L	F	N	G	Q	W	V	V	G	H	S	E	N	F	S	A	S	I	T	T	M	Q	A	V	I	W	I	V	T	F	L	A	M	L	A	L	T	I	F	I	R	Y	S	R	M
Secondary structure
SS confidence
Disorder																?		?	?	?	?	?	?	?	?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	R	A	C	R	A	C	A	E	D	L	K	M	A	S	L	L	G	I	N	T	D	R	V	I	A	L	T	F	V	I	G	A	A	M	A	A	V	A	G	V	L	L	G	Q	F	Y	G	V	I	N	P	Y	I	G	F	M	A	G	M
Secondary structure
SS confidence
Disorder																																																	?							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		K	A	F	T	A	A	V	L	G	G	I	G	S	I	P	G	A	M	I	G	G	L	I	L	G	I	A	E	A	L	S	S	A	Y	L	S	T	E	Y	K	D	V	V	S	F	A	L	L	I	L	V	L	L	V	M	P	T	G	I	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		G	R	P	E	V	E	K	V
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: 4 - 295 Aligned: 265 Modelled: 286 Confidence: 96.8% Identity: 14% 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: 4 - 295 Aligned: 261 Modelled: 279 Confidence: 96.1% Identity: 14% 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 3pxp chain A Region: 175 - 207 Aligned: 33 Modelled: 32 Confidence: 26.4% Identity: 12% 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 3u5e chain L Region: 183 - 202 Aligned: 20 Modelled: 20 Confidence: 17.9% Identity: 25% 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 4a18 chain U Region: 183 - 202 Aligned: 20 Modelled: 20 Confidence: 16.9% 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 2e74 chain G domain 1 Region: 210 - 233 Aligned: 24 Modelled: 24 Confidence: 14.2% Identity: 21% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 1y6u chain A Region: 191 - 208 Aligned: 18 Modelled: 18 Confidence: 7.8% Identity: 11% PDB header:dna binding protein Chain: A: PDB Molecule:excisionase from transposon tn916; PDBTitle: the structure of the excisionase (xis) protein from2 conjugative transposon tn916 provides insights into the3 regulation of heterobivalent tyrosine recombinases Phyre2 PDB 1y9q chain A Region: 177 - 207 Aligned: 31 Modelled: 26 Confidence: 5.4% Identity: 13% PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, hth_3 family; PDBTitle: crystal structure of hth_3 family transcriptional regulator2 from vibrio cholerae Phyre2 1 d1l7va_ 2 c2nq2A_ 3 c3pxpA_ 4 c3u5eL_ 5 c4a18U_ 6 d2e74g1 7 c1y6uA_ 8 c1y9qA_

Detailed template information

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

1 d1l7va_ 96.8 14 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_ 96.1 14 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 c3pxpA_ 26.4 12 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 4 c3u5eL_ 17.9 25 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 5 c4a18U_ 16.9 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 6 d2e74g1 14.2 21 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 7 c1y6uA_ 7.8 11 PDB header:dna binding protein Chain: A: PDB Molecule:excisionase from transposon tn916; PDBTitle: the structure of the excisionase (xis) protein from2 conjugative transposon tn916 provides insights into the3 regulation of heterobivalent tyrosine recombinases 8 c1y9qA_ 5.4 13 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, hth_3 family; PDBTitle: crystal structure of hth_3 family transcriptional regulator2 from vibrio cholerae

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