Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	A	L	N	K	K	S	F	L	T	Y	L	K	E	G	G	I	Y	V	V	L	L	V	L	L	A	I	I	I	F	Q	D	P	T	F	L	S	L	L	N	L	S	N	I	L	T	Q	S	S	V	R	I	I	I	A	L	G	V	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	L	I	V	T	Q	G	T	D	L	S	A	G	R	Q	V	G	L	A	A	V	V	A	A	T	L	L	Q	S	M	D	N	A	N	K	V	F	P	E	M	A	T	M	P	I	A	L	V	I	L	I	V	C	A	I	G	A	V	I	G
Secondary structure
SS confidence
Disorder																																	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	I	N	G	L	I	I	A	Y	L	N	V	T	P	F	I	T	T	L	G	T	M	I	I	V	Y	G	I	N	S	L	Y	Y	D	F	V	G	A	S	P	I	S	G	F	D	S	G	F	S	T	F	A	Q	G	F	V	A	L	G	S
Secondary structure
SS confidence
Disorder																																					?	?	?	?																?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		F	R	L	S	Y	I	T	F	Y	A	L	I	A	V	A	F	V	W	V	L	W	N	K	T	R	F	G	K	N	I	F	A	I	G	G	N	P	E	A	A	K	V	S	G	V	N	V	G	L	N	L	L	M	I	Y	A	L	S	G	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		F	Y	A	F	G	G	M	L	E	A	G	R	I	G	S	A	T	N	N	L	G	F	M	Y	E	L	D	A	I	A	A	C	V	V	G	G	V	S	F	S	G	G	V	G	T	V	I	G	V	V	T	G	V	I	I	F	T	V	I	N
Secondary structure
SS confidence
Disorder															?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.
Sequence		Y	G	L	T	Y	I	G	V	N	P	Y	W	Q	Y	I	I	K	G	A	I	I	I	F	A	V	A	L	D	S	L	K	Y	A	R	K	K
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: 70 - 327 Aligned: 223 Modelled: 231 Confidence: 97.0% 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: 1 - 329 Aligned: 303 Modelled: 317 Confidence: 97.0% 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 3pxp chain A Region: 201 - 233 Aligned: 33 Modelled: 32 Confidence: 22.9% Identity: 18% 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 4a18 chain U Region: 209 - 228 Aligned: 20 Modelled: 20 Confidence: 17.9% 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 3u5e chain L Region: 209 - 228 Aligned: 20 Modelled: 20 Confidence: 17.4% 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 2e74 chain G domain 1 Region: 236 - 259 Aligned: 24 Modelled: 24 Confidence: 16.2% Identity: 29% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 1iie chain A Region: 1 - 19 Aligned: 19 Modelled: 19 Confidence: 12.7% Identity: 16% Fold: Class II MHC-associated invariant chain ectoplasmic trimerization domain Superfamily: Class II MHC-associated invariant chain ectoplasmic trimerization domain Family: Class II MHC-associated invariant chain ectoplasmic trimerization domain Phyre2 PDB 2rdd chain B Region: 310 - 336 Aligned: 27 Modelled: 27 Confidence: 8.7% Identity: 11% PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. Phyre2 PDB 1col chain A Region: 226 - 303 Aligned: 69 Modelled: 78 Confidence: 7.5% Identity: 16% Fold: Toxins' membrane translocation domains Superfamily: Colicin Family: Colicin Phyre2 PDB 1y6u chain A Region: 217 - 234 Aligned: 18 Modelled: 18 Confidence: 7.4% 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 3do9 chain C Region: 2 - 13 Aligned: 12 Modelled: 12 Confidence: 6.9% Identity: 33% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:upf0302 protein ba_1542/gbaa1542/bas1430; PDBTitle: crystal structure of protein ba1542 from bacillus anthracis2 str.ames Phyre2 PDB 2wpd chain P Region: 206 - 238 Aligned: 29 Modelled: 33 Confidence: 6.8% Identity: 28% PDB header:hydrolase Chain: P: PDB Molecule:atp synthase subunit 9, mitochondrial; PDBTitle: the mg.adp inhibited state of the yeast f1c10 atp synthase Phyre2 PDB 1a87 chain A Region: 226 - 306 Aligned: 71 Modelled: 81 Confidence: 6.7% Identity: 10% PDB header:bacteriocin Chain: A: PDB Molecule:colicin n; PDBTitle: colicin n Phyre2 PDB 1a87 chain A Region: 226 - 306 Aligned: 71 Modelled: 81 Confidence: 6.7% Identity: 10% Fold: Toxins' membrane translocation domains Superfamily: Colicin Family: Colicin Phyre2 PDB 1vf5 chain G Region: 236 - 255 Aligned: 20 Modelled: 20 Confidence: 6.5% Identity: 30% 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: 236 - 255 Aligned: 20 Modelled: 20 Confidence: 6.5% Identity: 30% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 1mn8 chain A Region: 202 - 236 Aligned: 35 Modelled: 35 Confidence: 6.2% Identity: 11% Fold: Retroviral matrix proteins Superfamily: Retroviral matrix proteins Family: MMLV matrix protein-like Phyre2 PDB 1wur chain A domain 1 Region: 210 - 239 Aligned: 30 Modelled: 30 Confidence: 5.9% Identity: 13% Fold: T-fold Superfamily: Tetrahydrobiopterin biosynthesis enzymes-like Family: GTP cyclohydrolase I Phyre2 PDB 2iub chain A domain 2 Region: 179 - 205 Aligned: 27 Modelled: 27 Confidence: 5.7% Identity: 11% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 PDB 1y9q chain A Region: 203 - 233 Aligned: 31 Modelled: 26 Confidence: 5.7% 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 c2nq2A_ 2 d1l7va_ 3 c3pxpA_ 4 c4a18U_ 5 c3u5eL_ 6 d2e74g1 7 d1iiea_ 8 c2rddB_ 9 d1cola_ 10 c1y6uA_ 11 c3do9C_ 12 c2wpdP_ 13 c1a87A_ 14 d1a87a_ 15 c1vf5G_ 16 d1vf5g_ 17 d1mn8a_ 18 d1wura1 19 d2iuba2 20 c1y9qA_ 21 22 23 24

Detailed template information

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

1 c2nq2A_ 97.0 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_ 97.0 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 c3pxpA_ 22.9 18 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 c4a18U_ 17.9 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 5 c3u5eL_ 17.4 25 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 6 d2e74g1 16.2 29 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 7 d1iiea_ 12.7 16 Fold:Class II MHC-associated invariant chain ectoplasmic trimerization domain Superfamily:Class II MHC-associated invariant chain ectoplasmic trimerization domain Family:Class II MHC-associated invariant chain ectoplasmic trimerization domain 8 c2rddB_ 8.7 11 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. 9 d1cola_ 7.5 16 Fold:Toxins' membrane translocation domains Superfamily:Colicin Family:Colicin 10 c1y6uA_ 7.4 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 11 c3do9C_ 6.9 33 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:upf0302 protein ba_1542/gbaa1542/bas1430; PDBTitle: crystal structure of protein ba1542 from bacillus anthracis2 str.ames 12 c2wpdP_ 6.8 28 PDB header:hydrolase Chain: P: PDB Molecule:atp synthase subunit 9, mitochondrial; PDBTitle: the mg.adp inhibited state of the yeast f1c10 atp synthase 13 c1a87A_ 6.7 10 PDB header:bacteriocin Chain: A: PDB Molecule:colicin n; PDBTitle: colicin n 14 d1a87a_ 6.7 10 Fold:Toxins' membrane translocation domains Superfamily:Colicin Family:Colicin 15 c1vf5G_ 6.5 30 PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 16 d1vf5g_ 6.5 30 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 17 d1mn8a_ 6.2 11 Fold:Retroviral matrix proteins Superfamily:Retroviral matrix proteins Family:MMLV matrix protein-like 18 d1wura1 5.9 13 Fold:T-fold Superfamily:Tetrahydrobiopterin biosynthesis enzymes-like Family:GTP cyclohydrolase I 19 d2iuba2 5.7 11 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 20 c1y9qA_ 5.7 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 21 c3fewX_ not modelled 5.6 16 PDB header:immune system Chain: X: PDB Molecule:colicin s4; PDBTitle: structure and function of colicin s4, a colicin with a2 duplicated receptor binding domain 22 c1t5qA_ not modelled 5.6 23 PDB header:hormone/growth factor Chain: A: PDB Molecule:gastric inhibitory polypeptide; PDBTitle: solution structure of gip(1-30)amide in tfe/water 23 c2kfsA_ not modelled 5.5 33 PDB header:dna-binding protein Chain: A: PDB Molecule:conserved hypothetical regulatory protein; PDBTitle: nmr structure of rv2175c 24 c2b2hA_ not modelled 5.5 9 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as)

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