Secondary structure and disorder prediction

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Sequence		M	D	Q	A	L	L	D	G	G	Y	R	C	Y	T	G	E	K	I	D	V	Y	F	N	T	A	I	C	Q	H	S	G	N	C	V	R	G	N	G	K	L	F	N	L	K	R	K	P	W	I	M	P	D	E	V	D	V	A	T	V	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?																															?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.
Sequence		K	V	I	D	T	C	P	S	G	A	L	K	Y	R	H	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 1fxr chain A Region: 19 - 76 Aligned: 58 Modelled: 58 Confidence: 99.5% Identity: 17% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Single 4Fe-4S cluster ferredoxin Phyre2 PDB 1iqz chain A Region: 19 - 76 Aligned: 58 Modelled: 58 Confidence: 99.3% Identity: 12% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Single 4Fe-4S cluster ferredoxin Phyre2 PDB 1sj1 chain A Region: 17 - 75 Aligned: 59 Modelled: 59 Confidence: 99.3% Identity: 15% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Single 4Fe-4S cluster ferredoxin Phyre2 PDB 1dwl chain A Region: 19 - 73 Aligned: 55 Modelled: 55 Confidence: 99.2% Identity: 16% PDB header:electron transfer Chain: A: PDB Molecule:ferredoxin i; PDBTitle: the ferredoxin-cytochrome complex using heteronuclear nmr2 and docking simulation Phyre2 PDB 1vjw chain A Region: 20 - 73 Aligned: 54 Modelled: 54 Confidence: 99.1% Identity: 24% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Single 4Fe-4S cluster ferredoxin Phyre2 PDB 1fxd chain A Region: 25 - 72 Aligned: 47 Modelled: 48 Confidence: 98.4% Identity: 23% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Single 4Fe-4S cluster ferredoxin Phyre2 PDB 1kqf chain B Region: 8 - 73 Aligned: 66 Modelled: 66 Confidence: 97.7% Identity: 21% PDB header:oxidoreductase Chain: B: PDB Molecule:formate dehydrogenase, nitrate-inducible, iron-sulfur PDBTitle: formate dehydrogenase n from e. coli Phyre2 PDB 1kqf chain B domain 1 Region: 8 - 75 Aligned: 68 Modelled: 68 Confidence: 97.7% Identity: 21% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Ferredoxin domains from multidomain proteins Phyre2 PDB 1ti2 chain F Region: 12 - 75 Aligned: 62 Modelled: 64 Confidence: 97.6% Identity: 10% PDB header:oxidoreductase Chain: F: PDB Molecule:pyrogallol hydroxytransferase small subunit; PDBTitle: crystal structure of pyrogallol-phloroglucinol2 transhydroxylase from pelobacter acidigallici Phyre2 PDB 1gte chain A domain 5 Region: 16 - 76 Aligned: 61 Modelled: 61 Confidence: 97.6% Identity: 11% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Ferredoxin domains from multidomain proteins Phyre2 PDB 2vpy chain B Region: 13 - 75 Aligned: 63 Modelled: 63 Confidence: 97.6% Identity: 17% PDB header:oxidoreductase Chain: B: PDB Molecule:nrfc protein; PDBTitle: polysulfide reductase with bound quinone inhibitor,2 pentachlorophenol (pcp) Phyre2 PDB 1xer chain A Region: 20 - 73 Aligned: 54 Modelled: 54 Confidence: 97.4% Identity: 20% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Archaeal ferredoxins Phyre2 PDB 2fug chain 3 domain 4 Region: 20 - 72 Aligned: 53 Modelled: 53 Confidence: 97.4% Identity: 28% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Ferredoxin domains from multidomain proteins Phyre2 PDB 1gth chain D Region: 10 - 76 Aligned: 67 Modelled: 67 Confidence: 97.3% Identity: 10% PDB header:oxidoreductase Chain: D: PDB Molecule:dihydropyrimidine dehydrogenase; PDBTitle: dihydropyrimidine dehydrogenase (dpd) from pig, ternary2 complex with nadph and 5-iodouracil Phyre2 PDB 3gyx chain J Region: 20 - 74 Aligned: 55 Modelled: 55 Confidence: 97.2% Identity: 24% PDB header:oxidoreductase Chain: J: PDB Molecule:adenylylsulfate reductase; PDBTitle: crystal structure of adenylylsulfate reductase from2 desulfovibrio gigas Phyre2 PDB 1c4c chain A Region: 20 - 74 Aligned: 55 Modelled: 55 Confidence: 97.2% Identity: 25% PDB header:oxidoreductase Chain: A: PDB Molecule:protein (fe-only hydrogenase); PDBTitle: binding of exogenously added carbon monoxide at the active2 site of the fe-only hydrogenase (cpi) from clostridium3 pasteurianum Phyre2 PDB 2fug chain C Region: 20 - 72 Aligned: 53 Modelled: 53 Confidence: 97.2% Identity: 28% PDB header:oxidoreductase Chain: C: PDB Molecule:nadh-quinone oxidoreductase chain 3; PDBTitle: crystal structure of the hydrophilic domain of respiratory complex i2 from thermus thermophilus Phyre2 PDB 3c8y chain A domain 3 Region: 20 - 74 Aligned: 55 Modelled: 55 Confidence: 97.2% Identity: 20% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Ferredoxin domains from multidomain proteins Phyre2 PDB 1vlf chain N domain 2 Region: 12 - 75 Aligned: 59 Modelled: 64 Confidence: 96.9% Identity: 10% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Ferredoxin domains from multidomain proteins Phyre2 PDB 1jnr chain B Region: 20 - 74 Aligned: 55 Modelled: 55 Confidence: 96.9% Identity: 16% Fold: Ferredoxin-like Superfamily: 4Fe-4S ferredoxins Family: Ferredoxin domains from multidomain proteins Phyre2 PDB 2c3y chain A Region: 11 - 38 Aligned: 28 Modelled: 28 Confidence: 96.5% Identity: 29% PDB header:oxidoreductase Chain: A: PDB Molecule:pyruvate-ferredoxin oxidoreductase; PDBTitle: crystal structure of the radical form of2 pyruvate:ferredoxin oxidoreductase from desulfovibrio3 africanus Phyre2 1 d1fxra_ 2 d1iqza_ 3 d1sj1a_ 4 c1dwlA_ 5 d1vjwa_ 6 d1fxda_ 7 c1kqfB_ 8 d1kqfb1 9 c1ti2F_ 10 d1gtea5 11 c2vpyB_ 12 d1xera_ 13 d2fug34 14 c1gthD_ 15 c3gyxJ_ 16 c1c4cA_ 17 c2fugC_ 18 d3c8ya3 19 d1vlfn2 20 d1jnrb_ 21 22 23 24 25 c2c3yA_ 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69

Detailed template information

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

1 d1fxra_ 99.5 17 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Single 4Fe-4S cluster ferredoxin 2 d1iqza_ 99.3 12 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Single 4Fe-4S cluster ferredoxin 3 d1sj1a_ 99.3 15 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Single 4Fe-4S cluster ferredoxin 4 c1dwlA_ 99.2 16 PDB header:electron transfer Chain: A: PDB Molecule:ferredoxin i; PDBTitle: the ferredoxin-cytochrome complex using heteronuclear nmr2 and docking simulation 5 d1vjwa_ 99.1 24 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Single 4Fe-4S cluster ferredoxin 6 d1fxda_ 98.4 23 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Single 4Fe-4S cluster ferredoxin 7 c1kqfB_ 97.7 21 PDB header:oxidoreductase Chain: B: PDB Molecule:formate dehydrogenase, nitrate-inducible, iron-sulfur PDBTitle: formate dehydrogenase n from e. coli 8 d1kqfb1 97.7 21 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 9 c1ti2F_ 97.6 10 PDB header:oxidoreductase Chain: F: PDB Molecule:pyrogallol hydroxytransferase small subunit; PDBTitle: crystal structure of pyrogallol-phloroglucinol2 transhydroxylase from pelobacter acidigallici 10 d1gtea5 97.6 11 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 11 c2vpyB_ 97.6 17 PDB header:oxidoreductase Chain: B: PDB Molecule:nrfc protein; PDBTitle: polysulfide reductase with bound quinone inhibitor,2 pentachlorophenol (pcp) 12 d1xera_ 97.4 20 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Archaeal ferredoxins 13 d2fug34 97.4 28 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 14 c1gthD_ 97.3 10 PDB header:oxidoreductase Chain: D: PDB Molecule:dihydropyrimidine dehydrogenase; PDBTitle: dihydropyrimidine dehydrogenase (dpd) from pig, ternary2 complex with nadph and 5-iodouracil 15 c3gyxJ_ 97.2 24 PDB header:oxidoreductase Chain: J: PDB Molecule:adenylylsulfate reductase; PDBTitle: crystal structure of adenylylsulfate reductase from2 desulfovibrio gigas 16 c1c4cA_ 97.2 25 PDB header:oxidoreductase Chain: A: PDB Molecule:protein (fe-only hydrogenase); PDBTitle: binding of exogenously added carbon monoxide at the active2 site of the fe-only hydrogenase (cpi) from clostridium3 pasteurianum 17 c2fugC_ 97.2 28 PDB header:oxidoreductase Chain: C: PDB Molecule:nadh-quinone oxidoreductase chain 3; PDBTitle: crystal structure of the hydrophilic domain of respiratory complex i2 from thermus thermophilus 18 d3c8ya3 97.2 20 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 19 d1vlfn2 96.9 10 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 20 d1jnrb_ 96.9 16 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 21 c2ivfB_ not modelled 96.8 15 PDB header:oxidoreductase Chain: B: PDB Molecule:ethylbenzene dehydrogenase beta-subunit; PDBTitle: ethylbenzene dehydrogenase from aromatoleum aromaticum 22 d1h0hb_ not modelled 96.8 14 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 23 d2fug91 not modelled 96.6 14 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 24 c2fugG_ not modelled 96.6 14 PDB header:oxidoreductase Chain: G: PDB Molecule:nadh-quinone oxidoreductase chain 9; PDBTitle: crystal structure of the hydrophilic domain of respiratory complex i2 from thermus thermophilus 25 c2c3yA_ 96.5 29 PDB header:oxidoreductase Chain: A: PDB Molecule:pyruvate-ferredoxin oxidoreductase; PDBTitle: crystal structure of the radical form of2 pyruvate:ferredoxin oxidoreductase from desulfovibrio3 africanus 26 d1hfel2 not modelled 96.2 15 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 27 d1jb0c_ not modelled 96.1 16 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:7-Fe ferredoxin 28 c1hfeL_ not modelled 96.1 15 PDB header:hydrogenase Chain: L: PDB Molecule:protein (fe-only hydrogenase (e.c.1.18.99.1) PDBTitle: 1.6 a resolution structure of the fe-only hydrogenase from2 desulfovibrio desulfuricans 29 d1dura_ not modelled 96.0 17 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Short-chain ferredoxins 30 c1gx7A_ not modelled 95.7 17 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 31 c2fgoA_ not modelled 95.7 11 PDB header:electron transport Chain: A: PDB Molecule:ferredoxin; PDBTitle: structure of the 2[4fe-4s] ferredoxin from pseudomonas2 aeruginosa 32 c2zvsB_ not modelled 95.2 11 PDB header:electron transport Chain: B: PDB Molecule:uncharacterized ferredoxin-like protein yfhl; PDBTitle: crystal structure of the 2[4fe-4s] ferredoxin from escherichia coli 33 c2gmhA_ not modelled 95.2 19 PDB header:oxidoreductase Chain: A: PDB Molecule:electron transfer flavoprotein-ubiquinone PDBTitle: structure of porcine electron transfer flavoprotein-2 ubiquinone oxidoreductase in complexed with ubiquinone 34 d2fdna_ not modelled 94.7 15 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Short-chain ferredoxins 35 d1h98a_ not modelled 94.5 11 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:7-Fe ferredoxin 36 d7fd1a_ not modelled 94.5 13 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:7-Fe ferredoxin 37 c2v4jE_ not modelled 94.5 15 PDB header:oxidoreductase Chain: E: PDB Molecule:sulfite reductase, dissimilatory-type subunit PDBTitle: the crystal structure of desulfovibrio vulgaris2 dissimilatory sulfite reductase bound to dsrc provides3 novel insights into the mechanism of sulfate respiration 38 d1blua_ not modelled 94.4 11 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Short-chain ferredoxins 39 d1rgva_ not modelled 93.8 15 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Short-chain ferredoxins 40 c2v2kB_ not modelled 93.7 13 PDB header:electron transport Chain: B: PDB Molecule:ferredoxin; PDBTitle: the crystal structure of fdxa, a 7fe ferredoxin from2 mycobacterium smegmatis 41 d1y5ib1 not modelled 93.5 19 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 42 d3c7bb1 not modelled 93.2 16 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 43 d2c42a5 not modelled 92.7 25 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 44 d1fcaa_ not modelled 92.6 15 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Short-chain ferredoxins 45 d2gmha3 not modelled 92.2 20 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:ETF-QO domain-like 46 c3c7bE_ not modelled 92.0 16 PDB header:oxidoreductase Chain: E: PDB Molecule:sulfite reductase, dissimilatory-type subunit beta; PDBTitle: structure of the dissimilatory sulfite reductase from archaeoglobus2 fulgidus 47 c3bk7A_ not modelled 91.0 23 PDB header:hydrolyase/translation Chain: A: PDB Molecule:abc transporter atp-binding protein; PDBTitle: structure of the complete abce1/rnaase-l inhibitor protein2 from pyrococcus abysii 48 d1bc6a_ not modelled 90.4 21 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:7-Fe ferredoxin 49 c2v4jA_ not modelled 85.1 10 PDB header:oxidoreductase Chain: A: PDB Molecule:sulfite reductase, dissimilatory-type subunit PDBTitle: the crystal structure of desulfovibrio vulgaris2 dissimilatory sulfite reductase bound to dsrc provides3 novel insights into the mechanism of sulfate respiration 50 c3c7bA_ not modelled 84.8 10 PDB header:oxidoreductase Chain: A: PDB Molecule:sulfite reductase, dissimilatory-type subunit alpha; PDBTitle: structure of the dissimilatory sulfite reductase from archaeoglobus2 fulgidus 51 d2v4jb1 not modelled 80.2 19 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 52 d1clfa_ not modelled 75.2 21 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Short-chain ferredoxins 53 d2bs2b1 not modelled 48.2 25 Fold:Globin-like Superfamily:alpha-helical ferredoxin Family:Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain 54 d1kf6b1 not modelled 46.6 16 Fold:Globin-like Superfamily:alpha-helical ferredoxin Family:Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain 55 c1nekB_ not modelled 42.5 13 PDB header:oxidoreductase/electron transport Chain: B: PDB Molecule:succinate dehydrogenase iron-sulfur protein; PDBTitle: complex ii (succinate dehydrogenase) from e. coli with2 ubiquinone bound 56 c2bs2E_ not modelled 36.0 17 PDB header:oxidoreductase Chain: E: PDB Molecule:quinol-fumarate reductase iron-sulfur subunit b; PDBTitle: quinol:fumarate reductase from wolinella succinogenes 57 d1nekb1 not modelled 29.1 29 Fold:Globin-like Superfamily:alpha-helical ferredoxin Family:Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain 58 c2qwuB_ not modelled 20.8 35 PDB header:cell invasion Chain: B: PDB Molecule:intracellular growth locus, subunit c; PDBTitle: crystal structure of f. tularensis pathogenicity island2 protein c 59 c3cf4A_ not modelled 19.3 20 PDB header:oxidoreductase Chain: A: PDB Molecule:acetyl-coa decarboxylase/synthase alpha subunit; PDBTitle: structure of the codh component of the m. barkeri acds complex 60 c2vdcI_ not modelled 17.4 21 PDB header:oxidoreductase Chain: I: PDB Molecule:glutamate synthase [nadph] small chain; PDBTitle: the 9.5 a resolution structure of glutamate synthase from2 cryo-electron microscopy and its oligomerization behavior3 in solution: functional implications. 61 c2b76N_ not modelled 14.2 21 PDB header:oxidoreductase Chain: N: PDB Molecule:fumarate reductase iron-sulfur protein; PDBTitle: e. coli quinol fumarate reductase frda e49q mutation 62 c2h89B_ not modelled 13.5 29 PDB header:oxidoreductase Chain: B: PDB Molecule:succinate dehydrogenase ip subunit; PDBTitle: avian respiratory complex ii with malonate bound 63 d3c7ba1 not modelled 13.3 14 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 64 d2v4ja1 not modelled 11.0 11 Fold:Ferredoxin-like Superfamily:4Fe-4S ferredoxins Family:Ferredoxin domains from multidomain proteins 65 c3d6rA_ not modelled 7.7 56 PDB header:viral protein Chain: A: PDB Molecule:non-structural protein 1; PDBTitle: structure of an avian influenza a virus ns1 protein2 effector domain 66 c2z8nB_ not modelled 6.1 14 PDB header:lyase Chain: B: PDB Molecule:27.5 kda virulence protein; PDBTitle: structural basis for the catalytic mechanism of phosphothreonine lyase 67 d1ycya1 not modelled 5.8 28 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:PF1955-like 68 c1icfA_ not modelled 5.3 13 PDB header:hydrolase Chain: A: PDB Molecule:protein (cathepsin l: heavy chain); PDBTitle: crystal structure of mhc class ii associated p41 ii fragment in2 complex with cathepsin l 69 c3ktbD_ not modelled 5.3 38 PDB header:transcription regulator Chain: D: PDB Molecule:arsenical resistance operon trans-acting repressor; PDBTitle: crystal structure of arsenical resistance operon trans-acting2 repressor from bacteroides vulgatus atcc 8482

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