Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	G	F	T	T	R	V	K	S	E	A	S	E	K	K	P	F	N	F	A	L	F	W	D	K	Y	G	T	F	F	I	L	A	I	I	V	A	I	F	G	S	L	S	P	E	Y	F	L	T	T	N	N	I	T	Q	I	F	V	Q	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	V	T	V	L	I	G	M	G	E	F	F	A	I	L	V	A	G	I	D	L	S	V	G	A	I	L	A	L	S	G	M	V	T	A	K	L	M	L	A	G	V	D	P	F	L	A	A	M	I	G	G	V	L	V	G	G	A	L	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	I	N	G	C	L	V	N	W	T	G	L	H	P	F	I	I	T	L	G	T	N	A	I	F	R	G	I	T	L	V	I	S	D	A	N	S	V	Y	G	F	S	F	D	F	V	N	F	F	A	A	S	V	I	G	I	P	V	P	V
Secondary structure
SS confidence
Disorder																																					?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	F	S	L	I	V	A	L	I	L	W	F	L	T	T	R	M	R	L	G	R	N	I	Y	A	L	G	G	N	K	N	S	A	F	Y	S	G	I	D	V	K	F	H	I	L	V	V	F	I	I	S	G	V	C	A	G	L	A	G	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		V	S	T	A	R	L	G	A	A	E	P	L	A	G	M	G	F	E	T	Y	A	I	A	S	A	I	I	G	G	T	S	F	F	G	G	K	G	R	I	F	S	V	V	I	G	G	L	I	I	G	T	I	N	N	G	L	N	I	L	Q
Secondary structure
SS confidence
Disorder							?	?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.
Sequence		V	Q	T	Y	Y	Q	L	V	V	M	G	G	L	I	I	A	A	V	A	L	D	R	L	I	S	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: 90 - 320 Aligned: 218 Modelled: 219 Confidence: 97.9% 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: 15 - 322 Aligned: 291 Modelled: 296 Confidence: 96.6% 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 2b2h chain A Region: 8 - 223 Aligned: 207 Modelled: 216 Confidence: 76.9% Identity: 13% 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: 8 - 203 Aligned: 194 Modelled: 196 Confidence: 56.3% Identity: 15% Fold: Ammonium transporter Superfamily: Ammonium transporter Family: Ammonium transporter Phyre2 PDB 2e74 chain G domain 1 Region: 229 - 252 Aligned: 24 Modelled: 24 Confidence: 21.0% Identity: 25% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 1pgl chain 2 domain 2 Region: 1 - 16 Aligned: 16 Modelled: 16 Confidence: 18.4% Identity: 13% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Comoviridae-like VP Phyre2 PDB 1ny7 chain 2 domain 2 Region: 1 - 16 Aligned: 16 Modelled: 16 Confidence: 18.4% Identity: 13% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Comoviridae-like VP Phyre2 PDB 3hd6 chain A Region: 8 - 201 Aligned: 189 Modelled: 194 Confidence: 16.5% Identity: 13% 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 3b9y chain A Region: 7 - 202 Aligned: 184 Modelled: 196 Confidence: 14.5% 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 3hd7 chain A Region: 11 - 49 Aligned: 39 Modelled: 39 Confidence: 12.2% Identity: 23% PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 Phyre2 PDB 3u5e chain L Region: 202 - 221 Aligned: 20 Modelled: 20 Confidence: 9.8% Identity: 30% 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 - 221 Aligned: 20 Modelled: 20 Confidence: 9.3% 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 3pxp chain A Region: 194 - 226 Aligned: 33 Modelled: 32 Confidence: 8.7% Identity: 15% 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 1vf5 chain G Region: 229 - 248 Aligned: 20 Modelled: 20 Confidence: 6.6% 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: 229 - 248 Aligned: 20 Modelled: 20 Confidence: 6.6% Identity: 25% PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 1y6u chain A Region: 210 - 227 Aligned: 18 Modelled: 18 Confidence: 6.5% Identity: 11% 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: 196 - 215 Aligned: 20 Modelled: 20 Confidence: 6.3% Identity: 20% Fold: Photosystem I subunit PsaD Superfamily: Photosystem I subunit PsaD Family: Photosystem I subunit PsaD Phyre2 PDB 3e0d chain A Region: 78 - 110 Aligned: 33 Modelled: 33 Confidence: 5.3% Identity: 27% PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase iii subunit alpha; PDBTitle: insights into the replisome from the crystral structure of2 the ternary complex of the eubacterial dna polymerase iii3 alpha-subunit Phyre2 1 c2nq2A_ 2 d1l7va_ 3 c2b2hA_ 4 d1u7ga_ 5 d2e74g1 6 d1pgl22 7 d1ny722 8 c3hd6A_ 9 c3b9yA_ 10 c3hd7A_ 11 c3u5eL_ 12 c4a18U_ 13 c3pxpA_ 14 d1vf5g_ 15 c1vf5G_ 16 c1y6uA_ 17 d1jb0d_ 18 c3e0dA_

Detailed template information

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

1 c2nq2A_ 97.9 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_ 96.6 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 c2b2hA_ 76.9 13 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 4 d1u7ga_ 56.3 15 Fold:Ammonium transporter Superfamily:Ammonium transporter Family:Ammonium transporter 5 d2e74g1 21.0 25 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 6 d1pgl22 18.4 13 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 7 d1ny722 18.4 13 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 8 c3hd6A_ 16.5 13 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg 9 c3b9yA_ 14.5 14 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 10 c3hd7A_ 12.2 23 PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 11 c3u5eL_ 9.8 30 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 12 c4a18U_ 9.3 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 13 c3pxpA_ 8.7 15 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 14 d1vf5g_ 6.6 25 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 15 c1vf5G_ 6.6 25 PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 16 c1y6uA_ 6.5 11 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 17 d1jb0d_ 6.3 20 Fold:Photosystem I subunit PsaD Superfamily:Photosystem I subunit PsaD Family:Photosystem I subunit PsaD 18 c3e0dA_ 5.3 27 PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase iii subunit alpha; PDBTitle: insights into the replisome from the crystral structure of2 the ternary complex of the eubacterial dna polymerase iii3 alpha-subunit

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