Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	N	L	N	P	C	M	T	C	G	A	C	C	A	F	F	R	V	S	F	Y	W	A	E	A	D	D	A	G	G	T	I	P	A	R	L	T	E	Q	I	S	P	F	H	R	C	M	S	G	T	N	Q	K	N	P	R	C	I	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																				?	?	?	?	?	?	?							?	?		?										?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.
Sequence		L	A	G	T	P	G	K	N	A	C	C	T	I	Y	K	N	R	S	S	T	C	R	E	F	A	M	S	G	E	N	G	V	V	N	E	A	C	N	R	A	R	A	K	Y	G	L	T	P	L
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 1wil chain A Region: 2 - 15 Aligned: 14 Modelled: 14 Confidence: 19.4% Identity: 29% Fold: FYVE/PHD zinc finger Superfamily: FYVE/PHD zinc finger Family: variant PHD-like domain Phyre2 PDB 1nek chain B domain 1 Region: 1 - 13 Aligned: 13 Modelled: 13 Confidence: 16.3% Identity: 31% Fold: Globin-like Superfamily: alpha-helical ferredoxin Family: Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain Phyre2 PDB 1urj chain A Region: 84 - 108 Aligned: 25 Modelled: 25 Confidence: 15.4% Identity: 24% Fold: Viral ssDNA binding protein Superfamily: Viral ssDNA binding protein Family: Viral ssDNA binding protein Phyre2 PDB 1kf6 chain B domain 1 Region: 1 - 13 Aligned: 13 Modelled: 13 Confidence: 15.0% Identity: 31% Fold: Globin-like Superfamily: alpha-helical ferredoxin Family: Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain Phyre2 PDB 2dlq chain A domain 2 Region: 5 - 13 Aligned: 9 Modelled: 9 Confidence: 12.6% Identity: 44% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 2c42 chain A domain 5 Region: 3 - 13 Aligned: 11 Modelled: 11 Confidence: 9.6% Identity: 55% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Ferredoxin domains from multidomain proteins Phyre2 PDB 3git chain A Region: 68 - 108 Aligned: 30 Modelled: 41 Confidence: 9.2% Identity: 23% PDB header:transferase Chain: A: PDB Molecule:carbon monoxide dehydrogenase/acetyl-coa synthase subunit PDBTitle: crystal structure of a truncated acetyl-coa synthase Phyre2 PDB 1v06 chain A Region: 83 - 107 Aligned: 25 Modelled: 25 Confidence: 9.0% Identity: 8% PDB header:dna-binding protein Chain: A: PDB Molecule:hmg box-containing protein 1; PDBTitle: axh domain of the transcription factor hbp1 from m.musculus Phyre2 PDB 2fao chain B Region: 21 - 79 Aligned: 58 Modelled: 59 Confidence: 7.1% Identity: 17% PDB header:hydrolase/transferase Chain: B: PDB Molecule:probable atp-dependent dna ligase; PDBTitle: crystal structure of pseudomonas aeruginosa ligd polymerase2 domain Phyre2 PDB 1xer chain A Region: 3 - 13 Aligned: 11 Modelled: 11 Confidence: 6.9% Identity: 27% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Archaeal ferredoxins Phyre2 PDB 1gx7 chain A Region: 3 - 13 Aligned: 11 Modelled: 11 Confidence: 6.7% Identity: 36% PDB header:oxidoreductase Chain: A: PDB Molecule:periplasmic [fe] hydrogenase large subunit; PDBTitle: best model of the electron transfer complex between2 cytochrome c3 and [fe]-hydrogenase Phyre2 PDB 2b76 chain N Region: 2 - 13 Aligned: 12 Modelled: 12 Confidence: 6.3% Identity: 25% PDB header:oxidoreductase Chain: N: PDB Molecule:fumarate reductase iron-sulfur protein; PDBTitle: e. coli quinol fumarate reductase frda e49q mutation Phyre2 PDB 2iru chain A Region: 21 - 79 Aligned: 58 Modelled: 59 Confidence: 6.2% Identity: 10% PDB header:transferase Chain: A: PDB Molecule:putative dna ligase-like protein rv0938/mt0965; PDBTitle: crystal structure of the polymerase domain from mycobacterium2 tuberculosis ligase d Phyre2 PDB 1jb0 chain C Region: 3 - 13 Aligned: 11 Modelled: 11 Confidence: 6.2% Identity: 27% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: 7-Fe ferredoxin Phyre2 PDB 1nnq chain A domain 2 Region: 1 - 11 Aligned: 11 Modelled: 11 Confidence: 5.7% Identity: 27% Fold: Rubredoxin-like Superfamily: Rubredoxin-like Family: Rubredoxin Phyre2 PDB 2xv7 chain A Region: 8 - 16 Aligned: 9 Modelled: 9 Confidence: 5.5% Identity: 44% PDB header:hormone Chain: A: PDB Molecule:vascular endothelial growth factor d; PDBTitle: crystal structure of vascular endothelial growth factor d Phyre2 PDB 1h98 chain A Region: 3 - 13 Aligned: 11 Modelled: 11 Confidence: 5.2% Identity: 45% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: 7-Fe ferredoxin Phyre2 PDB 3mjg chain B Region: 8 - 16 Aligned: 9 Modelled: 9 Confidence: 5.2% Identity: 33% PDB header:hormone/transferase Chain: B: PDB Molecule:platelet-derived growth factor subunit b; PDBTitle: the structure of a platelet derived growth factor receptor complex Phyre2 1 d1wila_ 2 d1nekb1 3 d1urja_ 4 d1kf6b1 5 d2dlqa2 6 d2c42a5 7 c3gitA_ 8 c1v06A_ 9 c2faoB_ 10 d1xera_ 11 c1gx7A_ 12 c2b76N_ 13 c2iruA_ 14 d1jb0c_ 15 d1nnqa2 16 c2xv7A_ 17 d1h98a_ 18 c3mjgB_

Detailed template information

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

1 d1wila_ 19.4 29 Fold:FYVE/PHD zinc finger Superfamily:FYVE/PHD zinc finger Family:variant PHD-like domain 2 d1nekb1 16.3 31 Fold:Globin-like Superfamily:alpha-helical ferredoxin Family:Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain 3 d1urja_ 15.4 24 Fold:Viral ssDNA binding protein Superfamily:Viral ssDNA binding protein Family:Viral ssDNA binding protein 4 d1kf6b1 15.0 31 Fold:Globin-like Superfamily:alpha-helical ferredoxin Family:Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain 5 d2dlqa2 12.6 44 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 6 d2c42a5 9.6 55 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 7 c3gitA_ 9.2 23 PDB header:transferase Chain: A: PDB Molecule:carbon monoxide dehydrogenase/acetyl-coa synthase subunit PDBTitle: crystal structure of a truncated acetyl-coa synthase 8 c1v06A_ 9.0 8 PDB header:dna-binding protein Chain: A: PDB Molecule:hmg box-containing protein 1; PDBTitle: axh domain of the transcription factor hbp1 from m.musculus 9 c2faoB_ 7.1 17 PDB header:hydrolase/transferase Chain: B: PDB Molecule:probable atp-dependent dna ligase; PDBTitle: crystal structure of pseudomonas aeruginosa ligd polymerase2 domain 10 d1xera_ 6.9 27 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Archaeal ferredoxins 11 c1gx7A_ 6.7 36 PDB header:oxidoreductase Chain: A: PDB Molecule:periplasmic [fe] hydrogenase large subunit; PDBTitle: best model of the electron transfer complex between2 cytochrome c3 and [fe]-hydrogenase 12 c2b76N_ 6.3 25 PDB header:oxidoreductase Chain: N: PDB Molecule:fumarate reductase iron-sulfur protein; PDBTitle: e. coli quinol fumarate reductase frda e49q mutation 13 c2iruA_ 6.2 10 PDB header:transferase Chain: A: PDB Molecule:putative dna ligase-like protein rv0938/mt0965; PDBTitle: crystal structure of the polymerase domain from mycobacterium2 tuberculosis ligase d 14 d1jb0c_ 6.2 27 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:7-Fe ferredoxin 15 d1nnqa2 5.7 27 Fold:Rubredoxin-like Superfamily:Rubredoxin-like Family:Rubredoxin 16 c2xv7A_ 5.5 44 PDB header:hormone Chain: A: PDB Molecule:vascular endothelial growth factor d; PDBTitle: crystal structure of vascular endothelial growth factor d 17 d1h98a_ 5.2 45 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:7-Fe ferredoxin 18 c3mjgB_ 5.2 33 PDB header:hormone/transferase Chain: B: PDB Molecule:platelet-derived growth factor subunit b; PDBTitle: the structure of a platelet derived growth factor receptor 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

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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