Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	N	R	K	W	I	L	T	S	L	V	M	T	F	F	G	I	P	I	L	A	Q	F	L	A	V	V	I	A	M	L	G	V	G	L	A	G	I	I	E	V	C	N	I	L	I	T	P	T	I	Y	L	L	L	K	I	F	M	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.
Sequence		A	L	G	A	L	M	L	F	F	S	G	R	V	G	N	V	P	E	F	C	Y	V	G	Y	D	G	V	G	F	A	V	I	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 1oed chain E Region: 7 - 79 Aligned: 73 Modelled: 73 Confidence: 21.8% Identity: 23% Fold: Neurotransmitter-gated ion-channel transmembrane pore Superfamily: Neurotransmitter-gated ion-channel transmembrane pore Family: Neurotransmitter-gated ion-channel transmembrane pore Phyre2 PDB 2y69 chain Y Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 18.0% Identity: 33% PDB header:electron transport Chain: Y: PDB Molecule:cytochrome c oxidase subunit 7c; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1ehk chain B domain 2 Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 17.4% Identity: 39% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1v54 chain L Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 15.7% Identity: 33% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Family: Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Phyre2 PDB 1ijd chain B Region: 15 - 28 Aligned: 14 Modelled: 14 Confidence: 12.6% Identity: 43% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 3l09 chain B Region: 9 - 17 Aligned: 9 Modelled: 9 Confidence: 10.0% Identity: 33% PDB header:transcription regulator Chain: B: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator2 (jann_22dec04_contig27_revised_gene3569) from jannaschia sp. ccs1 at3 2.81 a resolution Phyre2 PDB 1nkz chain B Region: 15 - 28 Aligned: 14 Modelled: 14 Confidence: 10.0% Identity: 43% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 3koj chain A Region: 69 - 81 Aligned: 13 Modelled: 13 Confidence: 9.0% Identity: 23% PDB header:dna binding protein Chain: A: PDB Molecule:uncharacterized protein ycf41; PDBTitle: crystal structure of the ssb domain of q5n255_synp6 protein2 from synechococcus sp. northeast structural genomics3 consortium target snr59a. Phyre2 PDB 2wvq chain A Region: 33 - 43 Aligned: 11 Modelled: 11 Confidence: 8.2% Identity: 36% PDB header:prion-binding protein Chain: A: PDB Molecule:small s protein; PDBTitle: structure of the het-s n-terminal domain. mutant d23a, p33h Phyre2 PDB 3sqg chain E Region: 20 - 44 Aligned: 25 Modelled: 25 Confidence: 7.6% Identity: 36% PDB header:transferase Chain: E: PDB Molecule:methyl-coenzyme m reductase, beta subunit; PDBTitle: crystal structure of a methyl-coenzyme m reductase purified from black2 sea mats Phyre2 PDB 2pil chain A Region: 25 - 39 Aligned: 14 Modelled: 15 Confidence: 5.8% Identity: 50% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 1 d1oede_ 2 c2y69Y_ 3 d1ehkb2 4 d1v54l_ 5 d1ijdb_ 6 c3l09B_ 7 d1nkzb_ 8 c3kojA_ 9 c2wvqA_ 10 c3sqgE_ 11 d2pila_

Detailed template information

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

1 d1oede_ 21.8 23 Fold:Neurotransmitter-gated ion-channel transmembrane pore Superfamily:Neurotransmitter-gated ion-channel transmembrane pore Family:Neurotransmitter-gated ion-channel transmembrane pore 2 c2y69Y_ 18.0 33 PDB header:electron transport Chain: Y: PDB Molecule:cytochrome c oxidase subunit 7c; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 3 d1ehkb2 17.4 39 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 4 d1v54l_ 15.7 33 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Family:Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) 5 d1ijdb_ 12.6 43 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 6 c3l09B_ 10.0 33 PDB header:transcription regulator Chain: B: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator2 (jann_22dec04_contig27_revised_gene3569) from jannaschia sp. ccs1 at3 2.81 a resolution 7 d1nkzb_ 10.0 43 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 8 c3kojA_ 9.0 23 PDB header:dna binding protein Chain: A: PDB Molecule:uncharacterized protein ycf41; PDBTitle: crystal structure of the ssb domain of q5n255_synp6 protein2 from synechococcus sp. northeast structural genomics3 consortium target snr59a. 9 c2wvqA_ 8.2 36 PDB header:prion-binding protein Chain: A: PDB Molecule:small s protein; PDBTitle: structure of the het-s n-terminal domain. mutant d23a, p33h 10 c3sqgE_ 7.6 36 PDB header:transferase Chain: E: PDB Molecule:methyl-coenzyme m reductase, beta subunit; PDBTitle: crystal structure of a methyl-coenzyme m reductase purified from black2 sea mats 11 d2pila_ 5.8 50 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin

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

---

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