Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	V	G	E	G	L	L	S	A	A	R	F	A	L	R	V	V	A	C	G	N	A	L	S	L	A	L	K	S	N	L	G	R	S	F	S	S	F	P	A	W	A	E	Y	L	I	A	D	S	F	E	N	S	G	A	F	E	S	D
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																																																?		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.
Sequence		G	G	G	G	R	I	T	Q	R	C	A	L	R	P	S	G	R	C	L	R	Q	R	S	L	A	D	A	R	A	E	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 1f3u chain A Region: 64 - 75 Aligned: 12 Modelled: 12 Confidence: 16.7% Identity: 42% Fold: triple barrel Superfamily: Rap30/74 interaction domains Family: Rap30/74 interaction domains Phyre2 PDB 2jdi chain A domain 3 Region: 39 - 68 Aligned: 30 Modelled: 30 Confidence: 12.9% Identity: 27% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: RecA protein-like (ATPase-domain) Phyre2 PDB 1ma1 chain A domain 2 Region: 20 - 55 Aligned: 36 Modelled: 36 Confidence: 12.3% Identity: 22% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 2rjb chain D Region: 64 - 90 Aligned: 27 Modelled: 27 Confidence: 12.2% Identity: 44% PDB header:structural genomics, unknown function Chain: D: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of uncharacterized protein ydcj (sf1787)2 from shigella flexneri which includes domain duf1338.3 northeast structural genomics consortium target sfr276 Phyre2 PDB 2w6f chain A Region: 39 - 76 Aligned: 38 Modelled: 38 Confidence: 11.8% Identity: 21% PDB header:hydrolase Chain: A: PDB Molecule:atp synthase subunit alpha heart isoform, PDBTitle: low resolution structures of bovine mitochondrial f1-atpase2 during controlled dehydration: hydration state 2. Phyre2 PDB 1w0j chain B Region: 39 - 76 Aligned: 38 Modelled: 38 Confidence: 10.7% Identity: 21% PDB header:hydrolase Chain: B: PDB Molecule:atp synthase alpha chain heart isoform, PDBTitle: beryllium fluoride inhibited bovine f1-atpase Phyre2 PDB 2r9v chain A Region: 39 - 76 Aligned: 38 Modelled: 38 Confidence: 10.3% Identity: 21% PDB header:hydrolase Chain: A: PDB Molecule:atp synthase subunit alpha; PDBTitle: crystal structure of atp synthase subunit alpha (tm1612) from2 thermotoga maritima at 2.10 a resolution Phyre2 PDB 1ix9 chain A domain 2 Region: 21 - 55 Aligned: 35 Modelled: 35 Confidence: 10.1% Identity: 31% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1b06 chain A domain 2 Region: 21 - 55 Aligned: 35 Modelled: 35 Confidence: 8.8% Identity: 26% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1sky chain B domain 3 Region: 39 - 68 Aligned: 30 Modelled: 30 Confidence: 8.7% Identity: 27% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: RecA protein-like (ATPase-domain) Phyre2 PDB 3hh7 chain A Region: 59 - 72 Aligned: 14 Modelled: 14 Confidence: 8.6% Identity: 43% PDB header:toxin Chain: A: PDB Molecule:muscarinic toxin-like protein 3 homolog; PDBTitle: structural and functional characterization of a novel2 homodimeric three-finger neurotoxin from the venom of3 ophiophagus hannah (king cobra) Phyre2 PDB 3h0d chain B Region: 29 - 66 Aligned: 38 Modelled: 38 Confidence: 8.2% Identity: 29% PDB header:transcription/dna Chain: B: PDB Molecule:ctsr; PDBTitle: crystal structure of ctsr in complex with a 26bp dna duplex Phyre2 PDB 1q9c chain A Region: 41 - 69 Aligned: 29 Modelled: 29 Confidence: 7.8% Identity: 28% Fold: Histone-fold Superfamily: Histone-fold Family: TBP-associated factors, TAFs Phyre2 PDB 1uer chain A domain 2 Region: 21 - 48 Aligned: 28 Modelled: 28 Confidence: 6.4% Identity: 25% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1wb8 chain A domain 2 Region: 21 - 55 Aligned: 35 Modelled: 35 Confidence: 6.4% Identity: 23% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 2nyb chain A domain 2 Region: 21 - 55 Aligned: 35 Modelled: 35 Confidence: 6.3% Identity: 23% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1fx0 chain A domain 3 Region: 39 - 68 Aligned: 30 Modelled: 30 Confidence: 5.8% Identity: 27% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: RecA protein-like (ATPase-domain) Phyre2 PDB 1dt0 chain A domain 2 Region: 21 - 48 Aligned: 28 Modelled: 28 Confidence: 5.8% Identity: 25% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 1 d1f3ua_ 2 d2jdia3 3 d1ma1a2 4 c2rjbD_ 5 c2w6fA_ 6 c1w0jB_ 7 c2r9vA_ 8 d1ix9a2 9 d1b06a2 10 d1skyb3 11 c3hh7A_ 12 c3h0dB_ 13 d1q9ca_ 14 d1uera2 15 d1wb8a2 16 d2nyba2 17 d1fx0a3 18 d1dt0a2

Detailed template information

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

1 d1f3ua_ 16.7 42 Fold:triple barrel Superfamily:Rap30/74 interaction domains Family:Rap30/74 interaction domains 2 d2jdia3 12.9 27 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain) 3 d1ma1a2 12.3 22 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 4 c2rjbD_ 12.2 44 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of uncharacterized protein ydcj (sf1787)2 from shigella flexneri which includes domain duf1338.3 northeast structural genomics consortium target sfr276 5 c2w6fA_ 11.8 21 PDB header:hydrolase Chain: A: PDB Molecule:atp synthase subunit alpha heart isoform, PDBTitle: low resolution structures of bovine mitochondrial f1-atpase2 during controlled dehydration: hydration state 2. 6 c1w0jB_ 10.7 21 PDB header:hydrolase Chain: B: PDB Molecule:atp synthase alpha chain heart isoform, PDBTitle: beryllium fluoride inhibited bovine f1-atpase 7 c2r9vA_ 10.3 21 PDB header:hydrolase Chain: A: PDB Molecule:atp synthase subunit alpha; PDBTitle: crystal structure of atp synthase subunit alpha (tm1612) from2 thermotoga maritima at 2.10 a resolution 8 d1ix9a2 10.1 31 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 9 d1b06a2 8.8 26 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 10 d1skyb3 8.7 27 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain) 11 c3hh7A_ 8.6 43 PDB header:toxin Chain: A: PDB Molecule:muscarinic toxin-like protein 3 homolog; PDBTitle: structural and functional characterization of a novel2 homodimeric three-finger neurotoxin from the venom of3 ophiophagus hannah (king cobra) 12 c3h0dB_ 8.2 29 PDB header:transcription/dna Chain: B: PDB Molecule:ctsr; PDBTitle: crystal structure of ctsr in complex with a 26bp dna duplex 13 d1q9ca_ 7.8 28 Fold:Histone-fold Superfamily:Histone-fold Family:TBP-associated factors, TAFs 14 d1uera2 6.4 25 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 15 d1wb8a2 6.4 23 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 16 d2nyba2 6.3 23 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 17 d1fx0a3 5.8 27 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain) 18 d1dt0a2 5.8 25 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-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

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