Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	A	S	S	L	P	L	P	Q	G	K	S	V	S	L	K	Q	F	V	S	R	H	I	N	E	I	G	L	L	V	V	I	A	I	L	Y	L	V	F	S	L	N	A	P	G	F	I	S	L	N	N	Q	M	N	V	L	R	D	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	T	I	G	I	A	A	W	A	M	T	L	I	I	I	S	G	E	I	D	V	S	V	G	P	M	V	A	F	V	S	V	C	L	A	F	L	L	Q	F	E	V	P	L	A	V	A	C	L	L	V	L	L	L	G	A	L	M	G	T
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	A	G	V	L	R	G	V	F	N	V	P	S	F	V	A	T	L	G	L	W	S	A	L	R	G	M	G	L	F	M	T	N	A	L	P	V	P	I	D	E	N	E	V	L	D	W	L	G	G	Q	F	L	G	V	P	V	S	A	L
Secondary structure
SS confidence
Disorder																																				?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	M	I	V	L	F	A	L	F	V	F	I	S	R	K	T	A	F	G	R	S	V	F	A	V	G	G	N	A	T	A	A	Q	L	C	G	I	N	V	R	R	V	R	I	L	I	F	T	L	S	G	L	L	A	A	V	T	G	I	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	A	A	R	L	G	S	G	N	A	G	A	A	N	G	L	E	F	D	V	I	A	A	V	V	V	G	G	T	A	L	S	G	G	R	G	S	L	F	G	T	L	L	G	V	L	V	I	T	L	I	G	N	G	L	V	L	L	G	I
Secondary structure
SS confidence
Disorder							?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.
Sequence		N	S	F	F	Q	Q	V	V	R	G	V	I	I	V	V	A	V	L	A	N	I	L	L	T	Q	R	S	S	K	A	K	R
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: 90 - 319 Aligned: 217 Modelled: 230 Confidence: 97.7% 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 1l7v chain A Region: 14 - 320 Aligned: 292 Modelled: 307 Confidence: 97.1% 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 2b2h chain A Region: 11 - 222 Aligned: 204 Modelled: 212 Confidence: 85.0% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 1u7g chain A Region: 11 - 197 Aligned: 187 Modelled: 187 Confidence: 55.0% Identity: 12% Fold: Ammonium transporter Superfamily: Ammonium transporter Family: Ammonium transporter Phyre2 PDB 2jwa chain A Region: 302 - 332 Aligned: 31 Modelled: 31 Confidence: 34.2% Identity: 29% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 2e74 chain G domain 1 Region: 228 - 251 Aligned: 24 Modelled: 24 Confidence: 16.4% Identity: 21% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 3p5n chain A Region: 223 - 332 Aligned: 101 Modelled: 110 Confidence: 13.5% Identity: 13% PDB header:transport protein Chain: A: PDB Molecule:riboflavin uptake protein; PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter Phyre2 PDB 3pxp chain A Region: 193 - 225 Aligned: 33 Modelled: 32 Confidence: 12.1% Identity: 24% 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: 209 - 226 Aligned: 18 Modelled: 18 Confidence: 10.9% Identity: 22% 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 1jb0 chain D Region: 195 - 214 Aligned: 20 Modelled: 20 Confidence: 9.3% Identity: 25% Fold: Photosystem I subunit PsaD Superfamily: Photosystem I subunit PsaD Family: Photosystem I subunit PsaD Phyre2 PDB 2k21 chain A Region: 304 - 331 Aligned: 28 Modelled: 28 Confidence: 9.0% Identity: 0% PDB header:membrane protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily e PDBTitle: nmr structure of human kcne1 in lmpg micelles at ph 6.0 and2 40 degree c Phyre2 PDB 1vf5 chain G Region: 228 - 247 Aligned: 20 Modelled: 20 Confidence: 6.9% Identity: 25% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 1vf5 chain G Region: 228 - 247 Aligned: 20 Modelled: 20 Confidence: 6.9% Identity: 25% PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 2l2t chain A Region: 309 - 332 Aligned: 24 Modelled: 24 Confidence: 6.7% Identity: 21% PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain Phyre2 PDB 2iub chain A domain 2 Region: 164 - 197 Aligned: 34 Modelled: 34 Confidence: 6.7% Identity: 21% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 PDB 1pw4 chain A Region: 218 - 331 Aligned: 100 Modelled: 114 Confidence: 6.5% Identity: 15% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 3hd6 chain A Region: 9 - 200 Aligned: 187 Modelled: 187 Confidence: 6.3% Identity: 11% PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg Phyre2 PDB 3u5e chain L Region: 202 - 219 Aligned: 18 Modelled: 18 Confidence: 5.9% Identity: 44% 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: 202 - 219 Aligned: 18 Modelled: 18 Confidence: 5.8% Identity: 44% 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 2o01 chain D Region: 195 - 209 Aligned: 15 Modelled: 15 Confidence: 5.6% Identity: 20% PDB header:photosynthesis Chain: D: PDB Molecule:photosystem i reaction center subunit ii, PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution Phyre2 1 c2nq2A_ 2 d1l7va_ 3 c2b2hA_ 4 d1u7ga_ 5 c2jwaA_ 6 d2e74g1 7 c3p5nA_ 8 c3pxpA_ 9 c1y6uA_ 10 d1jb0d_ 11 c2k21A_ 12 d1vf5g_ 13 c1vf5G_ 14 c2l2tA_ 15 d2iuba2 16 d1pw4a_ 17 c3hd6A_ 18 c3u5eL_ 19 c4a18U_ 20 c2o01D_ 21 22 23 24 25

Detailed template information

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

1 c2nq2A_ 97.7 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. 2 d1l7va_ 97.1 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 3 c2b2hA_ 85.0 11 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 4 d1u7ga_ 55.0 12 Fold:Ammonium transporter Superfamily:Ammonium transporter Family:Ammonium transporter 5 c2jwaA_ 34.2 29 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 6 d2e74g1 16.4 21 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 7 c3p5nA_ 13.5 13 PDB header:transport protein Chain: A: PDB Molecule:riboflavin uptake protein; PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter 8 c3pxpA_ 12.1 24 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 9 c1y6uA_ 10.9 22 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 10 d1jb0d_ 9.3 25 Fold:Photosystem I subunit PsaD Superfamily:Photosystem I subunit PsaD Family:Photosystem I subunit PsaD 11 c2k21A_ 9.0 0 PDB header:membrane protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily e PDBTitle: nmr structure of human kcne1 in lmpg micelles at ph 6.0 and2 40 degree c 12 d1vf5g_ 6.9 25 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 13 c1vf5G_ 6.9 25 PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 14 c2l2tA_ 6.7 21 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain 15 d2iuba2 6.7 21 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 16 d1pw4a_ 6.5 15 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 17 c3hd6A_ 6.3 11 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg 18 c3u5eL_ 5.9 44 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 19 c4a18U_ 5.8 44 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 20 c2o01D_ 5.6 20 PDB header:photosynthesis Chain: D: PDB Molecule:photosystem i reaction center subunit ii, PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution 21 c2wseD_ not modelled 5.6 20 PDB header:photosynthesis Chain: D: PDB Molecule:photosystem i reaction center subunit ii, PDBTitle: improved model of plant photosystem i 22 c2k9yB_ not modelled 5.6 22 PDB header:transferase Chain: B: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 23 c2k9yA_ not modelled 5.6 22 PDB header:transferase Chain: A: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 24 c1a87A_ not modelled 5.3 13 PDB header:bacteriocin Chain: A: PDB Molecule:colicin n; PDBTitle: colicin n 25 d1a87a_ not modelled 5.3 13 Fold:Toxins' membrane translocation domains Superfamily:Colicin Family:Colicin

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