Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	T	Q	T	V	S	G	R	R	Y	F	T	K	A	W	L	M	E	Q	K	S	L	I	A	L	L	V	L	I	A	I	V	S	T	L	S	P	N	F	F	T	I	N	N	L	F	N	I	L	Q	Q	T	S	V	N	A	I	M	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	G	M	T	L	V	I	L	T	S	G	I	D	L	S	V	G	S	L	L	A	L	T	G	A	V	A	A	S	I	V	G	I	E	V	N	A	L	V	A	V	A	A	A	L	A	L	G	A	A	I	G	A	V	T	G	V	I	V	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		K	G	R	V	Q	A	F	I	A	T	L	V	M	M	L	L	L	R	G	V	T	M	V	Y	T	N	G	S	P	V	N	T	G	F	T	E	N	A	D	L	F	G	W	F	G	I	G	R	P	L	G	V	P	T	P	V	W	I	M	G
Secondary structure
SS confidence
Disorder																														?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	V	F	L	A	A	W	Y	M	L	H	H	T	R	L	G	R	Y	I	Y	A	L	G	G	N	E	A	A	T	R	L	S	G	I	N	V	N	K	I	K	I	I	V	Y	S	L	C	G	L	L	A	S	L	A	G	I	I	E	V	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		R	L	S	S	A	Q	P	T	A	G	T	G	Y	E	L	D	A	I	A	A	V	V	L	G	G	T	S	L	A	G	G	K	G	R	I	V	G	T	L	I	G	A	L	I	L	G	F	L	N	N	G	L	N	L	L	G	V	S	S	Y
Secondary structure
SS confidence
Disorder				?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.
Sequence		Y	Q	M	I	V	K	A	V	V	I	L	L	A	V	L	V	D	N	K	K	Q
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 2nq2 chain A Region: 74 - 317 Aligned: 224 Modelled: 244 Confidence: 98.4% Identity: 11% 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 1l7v chain A Region: 9 - 318 Aligned: 290 Modelled: 297 Confidence: 97.9% Identity: 10% 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 1u7g chain A Region: 9 - 194 Aligned: 186 Modelled: 186 Confidence: 47.4% Identity: 13% Fold: Ammonium transporter Superfamily: Ammonium transporter Family: Ammonium transporter Phyre2 PDB 3pxp chain A Region: 190 - 222 Aligned: 33 Modelled: 32 Confidence: 17.0% Identity: 21% 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 1y6u chain A Region: 206 - 223 Aligned: 18 Modelled: 18 Confidence: 15.8% Identity: 28% 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 2e74 chain G domain 1 Region: 225 - 248 Aligned: 24 Modelled: 24 Confidence: 15.4% Identity: 25% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 3u5e chain L Region: 198 - 217 Aligned: 20 Modelled: 20 Confidence: 9.6% Identity: 35% 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: 198 - 217 Aligned: 20 Modelled: 20 Confidence: 9.2% Identity: 30% 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 2kfs chain A Region: 206 - 220 Aligned: 15 Modelled: 15 Confidence: 6.7% Identity: 27% PDB header:dna-binding protein Chain: A: PDB Molecule:conserved hypothetical regulatory protein; PDBTitle: nmr structure of rv2175c Phyre2 PDB 2iub chain A domain 2 Region: 162 - 194 Aligned: 33 Modelled: 33 Confidence: 6.6% Identity: 15% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 PDB 1etx chain A Region: 190 - 220 Aligned: 31 Modelled: 31 Confidence: 6.0% Identity: 23% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2r6g chain F domain 2 Region: 98 - 221 Aligned: 124 Modelled: 124 Confidence: 5.6% Identity: 11% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 1y9q chain A Region: 192 - 222 Aligned: 31 Modelled: 26 Confidence: 5.4% Identity: 16% 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 PDB 1vf5 chain G Region: 225 - 244 Aligned: 20 Modelled: 20 Confidence: 5.4% Identity: 25% PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 1vf5 chain G Region: 225 - 244 Aligned: 20 Modelled: 20 Confidence: 5.4% Identity: 25% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 1 c2nq2A_ 2 d1l7va_ 3 d1u7ga_ 4 c3pxpA_ 5 c1y6uA_ 6 d2e74g1 7 c3u5eL_ 8 c4a18U_ 9 c2kfsA_ 10 d2iuba2 11 d1etxa_ 12 d2r6gf2 13 c1y9qA_ 14 c1vf5G_ 15 d1vf5g_

Detailed template information

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

1 c2nq2A_ 98.4 11 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. 2 d1l7va_ 97.9 10 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 3 d1u7ga_ 47.4 13 Fold:Ammonium transporter Superfamily:Ammonium transporter Family:Ammonium transporter 4 c3pxpA_ 17.0 21 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 5 c1y6uA_ 15.8 28 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 6 d2e74g1 15.4 25 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 7 c3u5eL_ 9.6 35 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 8 c4a18U_ 9.2 30 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 9 c2kfsA_ 6.7 27 PDB header:dna-binding protein Chain: A: PDB Molecule:conserved hypothetical regulatory protein; PDBTitle: nmr structure of rv2175c 10 d2iuba2 6.6 15 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 11 d1etxa_ 6.0 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 12 d2r6gf2 5.6 11 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 13 c1y9qA_ 5.4 16 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 14 c1vf5G_ 5.4 25 PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 15 d1vf5g_ 5.4 25 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex

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