Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	S	V	S	T	S	G	S	G	A	P	K	S	S	F	S	F	G	R	I	W	D	Q	Y	G	M	L	V	V	F	A	V	L	F	I	A	C	A	I	F	V	P	N	F	A	T	F	I	N	M	K	G	L	G	L	A	I	S	M
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	G	M	V	A	C	G	M	L	F	C	L	A	S	G	D	F	D	L	S	V	A	S	V	I	A	C	A	G	V	T	T	A	V	V	I	N	L	T	E	S	L	W	I	G	V	A	A	G	L	L	L	G	V	L	C	G	L	V	N
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	F	V	I	A	K	L	K	I	N	A	L	I	T	T	L	A	T	M	Q	I	V	R	G	L	A	Y	I	I	S	D	G	K	A	V	G	I	E	D	E	S	F	F	A	L	G	Y	A	N	W	F	G	L	P	A	P	I	W	L	T
Secondary structure
SS confidence
Disorder																																		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	A	C	L	I	I	F	G	L	L	L	N	K	T	T	F	G	R	N	T	L	A	I	G	G	N	E	E	A	A	R	L	A	G	V	P	V	V	R	T	K	I	I	I	F	V	L	S	G	L	V	S	A	I	A	G	I	I	L	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		S	R	M	T	S	G	Q	P	M	T	S	I	G	Y	E	L	I	V	I	S	A	C	V	L	G	G	V	S	L	K	G	G	I	G	K	I	S	Y	V	V	A	G	I	L	I	L	G	T	V	E	N	A	M	N	L	L	N	I	S	P
Secondary structure
SS confidence
Disorder					?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.
Sequence		F	A	Q	Y	V	V	R	G	L	I	L	L	A	A	V	I	F	D	R	Y	K	Q	K	A	K	R	T	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 2nq2 chain A Region: 49 - 318 Aligned: 255 Modelled: 270 Confidence: 97.3% Identity: 13% 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: 19 - 318 Aligned: 285 Modelled: 288 Confidence: 97.1% 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 2e74 chain G domain 1 Region: 226 - 249 Aligned: 24 Modelled: 24 Confidence: 24.5% Identity: 21% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 2b2h chain A Region: 6 - 220 Aligned: 207 Modelled: 215 Confidence: 17.0% Identity: 12% 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: 191 - 223 Aligned: 33 Modelled: 32 Confidence: 11.6% 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 3u5e chain L Region: 200 - 218 Aligned: 19 Modelled: 19 Confidence: 11.4% Identity: 32% 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: 199 - 218 Aligned: 20 Modelled: 20 Confidence: 11.3% 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 1y6u chain A Region: 207 - 224 Aligned: 18 Modelled: 18 Confidence: 10.6% Identity: 17% 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 1u7g chain A Region: 6 - 200 Aligned: 194 Modelled: 195 Confidence: 8.8% Identity: 12% Fold: Ammonium transporter Superfamily: Ammonium transporter Family: Ammonium transporter Phyre2 PDB 3b9y chain A Region: 5 - 131 Aligned: 127 Modelled: 127 Confidence: 7.8% 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 1vf5 chain G Region: 226 - 245 Aligned: 20 Modelled: 20 Confidence: 7.6% Identity: 20% 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: 226 - 245 Aligned: 20 Modelled: 20 Confidence: 7.6% Identity: 20% PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 3p5n chain A Region: 221 - 327 Aligned: 101 Modelled: 107 Confidence: 6.3% Identity: 7% 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 2dt5 chain A domain 1 Region: 205 - 221 Aligned: 17 Modelled: 17 Confidence: 5.9% Identity: 24% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Transcriptional repressor Rex, N-terminal domain Phyre2 1 c2nq2A_ 2 d1l7va_ 3 d2e74g1 4 c2b2hA_ 5 c3pxpA_ 6 c3u5eL_ 7 c4a18U_ 8 c1y6uA_ 9 d1u7ga_ 10 c3b9yA_ 11 d1vf5g_ 12 c1vf5G_ 13 c3p5nA_ 14 d2dt5a1

Detailed template information

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

1 c2nq2A_ 97.3 13 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 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 3 d2e74g1 24.5 21 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 4 c2b2hA_ 17.0 12 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 5 c3pxpA_ 11.6 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 6 c3u5eL_ 11.4 32 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 7 c4a18U_ 11.3 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 c1y6uA_ 10.6 17 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 9 d1u7ga_ 8.8 12 Fold:Ammonium transporter Superfamily:Ammonium transporter Family:Ammonium transporter 10 c3b9yA_ 7.8 14 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 11 d1vf5g_ 7.6 20 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 12 c1vf5G_ 7.6 20 PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 13 c3p5nA_ 6.3 7 PDB header:transport protein Chain: A: PDB Molecule:riboflavin uptake protein; PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter 14 d2dt5a1 5.9 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional repressor Rex, N-terminal domain

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