Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	R	N	V	K	K	Q	R	P	V	N	L	D	L	Q	T	I	R	F	P	I	T	A	I	A	S	I	L	H	R	V	S	G	V	I	T	F	V	A	V	G	I	L	L	W	L	L	G	T	S	L	S	S	P	E	G	F	E	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	S	A	I	M	G	S	F	F	V	K	F	I	M	W	G	I	L	T	A	L	A	Y	H	V	V	V	G	I	R	H	M	M	M	D	F	G	Y	L	E	E	T	F	E	A	G	K	R	S	A	K	I	S	F	V	I	T	V	V	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.
Sequence		S	L	L	A	G	V	L	V	W
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 1nek chain C Region: 1 - 129 Aligned: 129 Modelled: 129 Confidence: 100.0% Identity: 100% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 1yq3 chain C Region: 3 - 127 Aligned: 124 Modelled: 125 Confidence: 100.0% Identity: 19% PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone Phyre2 PDB 1nek chain D Region: 23 - 128 Aligned: 100 Modelled: 106 Confidence: 98.7% Identity: 18% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 2bs2 chain C domain 1 Region: 19 - 128 Aligned: 110 Modelled: 110 Confidence: 97.6% Identity: 9% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Fumarate reductase respiratory complex cytochrome b subunit, FrdC Phyre2 PDB 1kf6 chain D Region: 2 - 128 Aligned: 110 Modelled: 127 Confidence: 96.2% Identity: 17% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 1kf6 chain C Region: 29 - 86 Aligned: 58 Modelled: 58 Confidence: 92.6% Identity: 17% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 2hde chain A Region: 6 - 21 Aligned: 15 Modelled: 16 Confidence: 19.9% Identity: 20% PDB header:transcription Chain: A: PDB Molecule:histone deacetylase complex subunit sap18; PDBTitle: solution structure of human sap18 Phyre2 PDB 1qmh chain A domain 2 Region: 2 - 34 Aligned: 29 Modelled: 30 Confidence: 17.7% Identity: 14% Fold: IF3-like Superfamily: EPT/RTPC-like Family: RNA 3'-terminal phosphate cyclase, RPTC Phyre2 PDB 2vfy chain A Region: 4 - 19 Aligned: 16 Modelled: 16 Confidence: 15.3% Identity: 13% PDB header:hydrolase Chain: A: PDB Molecule:akap18 delta; PDBTitle: akap18 delta central domain Phyre2 PDB 3c19 chain A Region: 4 - 10 Aligned: 7 Modelled: 7 Confidence: 14.8% Identity: 57% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein mk0293; PDBTitle: crystal structure of protein mk0293 from methanopyrus kandleri av19 Phyre2 PDB 3c25 chain A Region: 8 - 17 Aligned: 10 Modelled: 10 Confidence: 14.4% Identity: 30% PDB header:hydrolase/dna Chain: A: PDB Molecule:noti restriction endonuclease; PDBTitle: crystal structure of noti restriction endonuclease bound to cognate2 dna Phyre2 PDB 2ww9 chain O Region: 1 - 11 Aligned: 11 Modelled: 11 Confidence: 14.0% Identity: 36% PDB header:ribosome Chain: O: PDB Molecule:60s ribosomal protein l39; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome Phyre2 PDB 1iuh chain A Region: 2 - 19 Aligned: 18 Modelled: 18 Confidence: 13.3% Identity: 17% Fold: LigT-like Superfamily: LigT-like Family: 2'-5' RNA ligase LigT Phyre2 PDB 2f9j chain P Region: 7 - 12 Aligned: 6 Modelled: 6 Confidence: 12.8% Identity: 33% PDB header:rna binding protein Chain: P: PDB Molecule:splicing factor 3b subunit 1; PDBTitle: 3.0 angstrom resolution structure of a y22m mutant of the spliceosomal2 protein p14 bound to a region of sf3b155 Phyre2 PDB 2ojm chain A Region: 81 - 92 Aligned: 12 Modelled: 12 Confidence: 12.3% Identity: 33% PDB header:antimicrobial protein Chain: A: PDB Molecule:moronecidin; PDBTitle: solution structure and cell selectivity of piscidin 1 and2 its analogues Phyre2 PDB 3pqv chain D Region: 2 - 16 Aligned: 14 Modelled: 15 Confidence: 11.5% Identity: 21% PDB header:unknown function Chain: D: PDB Molecule:rcl1 protein; PDBTitle: cyclase homolog Phyre2 PDB 4a1b chain B Region: 1 - 11 Aligned: 11 Modelled: 11 Confidence: 9.1% Identity: 36% PDB header:ribosome Chain: B: PDB Molecule:rpl39; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 26s rrna and3 proteins of molecule 3. Phyre2 PDB 2pu9 chain B domain 1 Region: 7 - 17 Aligned: 11 Modelled: 11 Confidence: 8.5% Identity: 27% Fold: SH3-like barrel Superfamily: Electron transport accessory proteins Family: Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain Phyre2 PDB 2zkr chain 3 Region: 1 - 11 Aligned: 11 Modelled: 11 Confidence: 8.1% Identity: 27% PDB header:ribosomal protein/rna Chain: 3: PDB Molecule:60s ribosomal protein l39e; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map Phyre2 PDB 2wfo chain A Region: 87 - 92 Aligned: 6 Modelled: 6 Confidence: 7.7% Identity: 50% PDB header:viral protein Chain: A: PDB Molecule:glycoprotein 1; PDBTitle: crystal structure of machupo virus envelope glycoprotein2 gp1 Phyre2 1 d1nekc_ 2 c1yq3C_ 3 d1nekd_ 4 d2bs2c1 5 d1kf6d_ 6 d1kf6c_ 7 c2hdeA_ 8 d1qmha2 9 c2vfyA_ 10 c3c19A_ 11 c3c25A_ 12 c2ww9O_ 13 d1iuha_ 14 c2f9jP_ 15 c2ojmA_ 16 c3pqvD_ 17 c4a1bB_ 18 d2pu9b1 19 c2zkr3_ 20 c2wfoA_ 21 22 23 24 25 26 27

Detailed template information

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

1 d1nekc_ 100.0 100 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 2 c1yq3C_ 100.0 19 PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone 3 d1nekd_ 98.7 18 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 4 d2bs2c1 97.6 9 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Fumarate reductase respiratory complex cytochrome b subunit, FrdC 5 d1kf6d_ 96.2 17 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 6 d1kf6c_ 92.6 17 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 7 c2hdeA_ 19.9 20 PDB header:transcription Chain: A: PDB Molecule:histone deacetylase complex subunit sap18; PDBTitle: solution structure of human sap18 8 d1qmha2 17.7 14 Fold:IF3-like Superfamily:EPT/RTPC-like Family:RNA 3'-terminal phosphate cyclase, RPTC 9 c2vfyA_ 15.3 13 PDB header:hydrolase Chain: A: PDB Molecule:akap18 delta; PDBTitle: akap18 delta central domain 10 c3c19A_ 14.8 57 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein mk0293; PDBTitle: crystal structure of protein mk0293 from methanopyrus kandleri av19 11 c3c25A_ 14.4 30 PDB header:hydrolase/dna Chain: A: PDB Molecule:noti restriction endonuclease; PDBTitle: crystal structure of noti restriction endonuclease bound to cognate2 dna 12 c2ww9O_ 14.0 36 PDB header:ribosome Chain: O: PDB Molecule:60s ribosomal protein l39; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome 13 d1iuha_ 13.3 17 Fold:LigT-like Superfamily:LigT-like Family:2'-5' RNA ligase LigT 14 c2f9jP_ 12.8 33 PDB header:rna binding protein Chain: P: PDB Molecule:splicing factor 3b subunit 1; PDBTitle: 3.0 angstrom resolution structure of a y22m mutant of the spliceosomal2 protein p14 bound to a region of sf3b155 15 c2ojmA_ 12.3 33 PDB header:antimicrobial protein Chain: A: PDB Molecule:moronecidin; PDBTitle: solution structure and cell selectivity of piscidin 1 and2 its analogues 16 c3pqvD_ 11.5 21 PDB header:unknown function Chain: D: PDB Molecule:rcl1 protein; PDBTitle: cyclase homolog 17 c4a1bB_ 9.1 36 PDB header:ribosome Chain: B: PDB Molecule:rpl39; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 26s rrna and3 proteins of molecule 3. 18 d2pu9b1 8.5 27 Fold:SH3-like barrel Superfamily:Electron transport accessory proteins Family:Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain 19 c2zkr3_ 8.1 27 PDB header:ribosomal protein/rna Chain: 3: PDB Molecule:60s ribosomal protein l39e; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 20 c2wfoA_ 7.7 50 PDB header:viral protein Chain: A: PDB Molecule:glycoprotein 1; PDBTitle: crystal structure of machupo virus envelope glycoprotein2 gp1 21 d1rioa_ not modelled 7.1 25 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 22 d1jh6a_ not modelled 7.1 21 Fold:LigT-like Superfamily:LigT-like Family:tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase 23 c1qmiC_ not modelled 6.9 14 PDB header:rna 3'-terminal phosphate cyclase Chain: C: PDB Molecule:rna 3'-terminal phosphate cyclase; PDBTitle: crystal structure of rna 3'-terminal phosphate cyclase, an2 ubiquitous enzyme with unusual topology 24 c3dl8D_ not modelled 6.7 33 PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 25 d1eg3a2 not modelled 6.3 29 Fold:EF Hand-like Superfamily:EF-hand Family:EF-hand modules in multidomain proteins 26 c1jekA_ not modelled 5.8 33 PDB header:viral protein Chain: A: PDB Molecule:env polyprotein; PDBTitle: visna tm core structure 27 c2d4gA_ not modelled 5.8 0 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein bsu11850; PDBTitle: structure of yjcg protein, a putative 2'-5' rna ligase from2 bacillus subtilis

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