Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	I	R	Y	G	W	E	L	A	L	A	A	L	L	V	I	E	I	V	A	F	G	A	I	N	P	R	M	L	D	L	N	M	L	L	F	S	T	S	D	F	I	C	I	G	I	V	A	L	P	L	T	M	V	I	V	S	G	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	D	I	S	F	G	S	T	I	G	L	C	A	I	A	L	G	V	L	F	Q	S	G	V	P	M	P	L	A	I	L	L	T	L	L	L	G	A	L	C	G	L	I	N	A	G	L	I	I	Y	T	K	V	N	P	L	V	I	T	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	T	L	Y	L	F	A	G	S	A	L	L	L	S	G	M	A	G	A	T	G	Y	E	G	I	G	G	F	P	M	A	F	T	D	F	A	N	L	D	V	L	G	L	P	V	P	L	I	I	F	L	I	C	L	L	V	F	W	L	W
Secondary structure
SS confidence
Disorder																		?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	H	K	T	H	A	G	R	N	V	F	L	I	G	Q	S	P	R	V	A	L	Y	S	A	I	P	V	N	R	T	L	C	A	L	Y	A	M	T	G	L	A	S	A	V	A	A	V	L	L	V	S	Y	F	G	S	A	R	S	D	L
Secondary structure
SS confidence
Disorder																																																							?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		G	A	S	F	L	M	P	A	I	T	A	V	V	L	G	G	A	N	I	Y	G	G	S	G	S	I	I	G	T	A	I	A	V	L	L	V	G	Y	L	Q	Q	G	L	Q	M	A	G	V	P	N	Q	V	S	S	A	L	S	G	A	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330
Sequence		L	I	V	V	V	V	G	R	S	V	S	L	H	R	Q	Q	I	K	E	W	L	A	R	R	A	N	N	P	L	P
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: 5 - 308 Aligned: 285 Modelled: 292 Confidence: 97.4% 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: 2 - 308 Aligned: 288 Modelled: 307 Confidence: 97.2% 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 2b2h chain A Region: 12 - 210 Aligned: 191 Modelled: 199 Confidence: 65.3% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 2e74 chain G domain 1 Region: 216 - 239 Aligned: 24 Modelled: 24 Confidence: 18.7% Identity: 8% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 3pxp chain A Region: 181 - 210 Aligned: 30 Modelled: 29 Confidence: 15.5% Identity: 13% 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 2w8a chain C Region: 266 - 330 Aligned: 64 Modelled: 65 Confidence: 10.8% Identity: 16% PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate Phyre2 PDB 4a18 chain U Region: 189 - 208 Aligned: 20 Modelled: 20 Confidence: 9.8% 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: 189 - 208 Aligned: 20 Modelled: 20 Confidence: 9.4% 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 1y6u chain A Region: 197 - 214 Aligned: 18 Modelled: 18 Confidence: 7.2% 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 2ww9 chain O Region: 313 - 330 Aligned: 18 Modelled: 18 Confidence: 6.8% Identity: 39% PDB header:ribosome Chain: O: PDB Molecule:60s ribosomal protein l39; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome Phyre2 PDB 1vf5 chain G Region: 216 - 235 Aligned: 20 Modelled: 20 Confidence: 5.8% Identity: 5% 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: 216 - 235 Aligned: 20 Modelled: 20 Confidence: 5.8% Identity: 5% 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 c2b2hA_ 4 d2e74g1 5 c3pxpA_ 6 c2w8aC_ 7 c4a18U_ 8 c3u5eL_ 9 c1y6uA_ 10 c2ww9O_ 11 c1vf5G_ 12 d1vf5g_

Detailed template information

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

1 c2nq2A_ 97.4 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_ 97.2 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 c2b2hA_ 65.3 12 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 4 d2e74g1 18.7 8 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 5 c3pxpA_ 15.5 13 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 c2w8aC_ 10.8 16 PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate 7 c4a18U_ 9.8 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_ 9.4 25 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 9 c1y6uA_ 7.2 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 10 c2ww9O_ 6.8 39 PDB header:ribosome Chain: O: PDB Molecule:60s ribosomal protein l39; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome 11 c1vf5G_ 5.8 5 PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 12 d1vf5g_ 5.8 5 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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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