Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	Y	V	D	G	F	V	V	A	V	P	A	D	K	K	D	A	Y	R	E	M	A	A	K	A	A	P	L	F	K	E	F	G	A	L	R	I	V	E	C	W	A	S	D	V	P	D	G	K	V	T	D	F	R	M	A	V	K	A
Secondary structure
SS confidence
Disorder		?	?	?																																																?								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.
Sequence		E	E	N	E	E	V	V	F	S	W	I	E	Y	P	S	K	E	V	R	D	A	A	N	Q	K	M	M	S	D	P	R	M	K	E	F	G	E	S	M	P	F	D	G	K	R	M	I	Y	G	G	F	E	S	I	I	D	E
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 2okq chain A domain 1 Region: 1 - 117 Aligned: 117 Modelled: 117 Confidence: 100.0% Identity: 100% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: YbaA-like Phyre2 PDB 2okq chain B Region: 1 - 117 Aligned: 109 Modelled: 117 Confidence: 100.0% Identity: 100% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ybaa; PDBTitle: crystal structure of unknown conserved ybaa protein from2 shigella flexneri Phyre2 PDB 1vqs chain A Region: 11 - 94 Aligned: 68 Modelled: 70 Confidence: 87.4% Identity: 19% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: NIPSNAP Phyre2 PDB 1vqy chain A domain 1 Region: 11 - 94 Aligned: 68 Modelled: 70 Confidence: 86.1% Identity: 19% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: NIPSNAP Phyre2 PDB 2fiu chain A domain 1 Region: 7 - 84 Aligned: 65 Modelled: 78 Confidence: 80.5% Identity: 23% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: Atu0297-like Phyre2 PDB 3lo3 chain E Region: 7 - 81 Aligned: 62 Modelled: 75 Confidence: 75.2% Identity: 18% PDB header:structure genomics, unknown function Chain: E: PDB Molecule:uncharacterized conserved protein; PDBTitle: the crystal structure of a conserved functionally unknown2 protein from colwellia psychrerythraea 34h. Phyre2 PDB 2wgh chain A Region: 2 - 38 Aligned: 37 Modelled: 37 Confidence: 53.4% Identity: 14% PDB header:oxidoreductase Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large PDBTitle: human ribonucleotide reductase r1 subunit (rrm1) in complex2 with datp and mg. Phyre2 PDB 3nfq chain A Region: 28 - 55 Aligned: 28 Modelled: 28 Confidence: 52.2% Identity: 25% PDB header:transcription Chain: A: PDB Molecule:transcription factor iws1; PDBTitle: crystal structure of the conserved central domain of yeast spn1/iws1 Phyre2 PDB 2cvu chain A Region: 2 - 38 Aligned: 37 Modelled: 37 Confidence: 51.4% Identity: 19% PDB header:oxidoreductase Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large chain PDBTitle: structures of yeast ribonucleotide reductase i Phyre2 PDB 3hnf chain A Region: 2 - 38 Aligned: 37 Modelled: 37 Confidence: 45.2% Identity: 14% PDB header:oxidoreductase Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large subunit; PDBTitle: crystal structure of human ribonucleotide reductase 1 bound to the2 effectors ttp and datp Phyre2 PDB 2xpn chain A Region: 28 - 55 Aligned: 28 Modelled: 28 Confidence: 44.7% Identity: 18% PDB header:transcription Chain: A: PDB Molecule:iws1; PDBTitle: crystal structure of a spt6-iws1(spn1) complex from2 encephalitozoon cuniculi, form i Phyre2 PDB 3dca chain C Region: 12 - 81 Aligned: 58 Modelled: 58 Confidence: 33.2% Identity: 19% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:rpa0582; PDBTitle: crystal structure of the rpa0582- protein of unknown2 function from rhodopseudomonas palustris- a structural3 genomics target Phyre2 PDB 3bm7 chain A Region: 9 - 81 Aligned: 56 Modelled: 56 Confidence: 31.0% Identity: 21% PDB header:oxidoreductase Chain: A: PDB Molecule:protein of unknown function with ferredoxin-like fold; PDBTitle: crystal structure of a putative antibiotic biosynthesis monooxygenase2 (cc_2132) from caulobacter crescentus cb15 at 1.35 a resolution Phyre2 PDB 2ril chain A Region: 8 - 86 Aligned: 65 Modelled: 65 Confidence: 29.9% Identity: 22% PDB header:oxidoreductase Chain: A: PDB Molecule:antibiotic biosynthesis monooxygenase; PDBTitle: crystal structure of a putative monooxygenase (yp_001095275.1) from2 shewanella loihica pv-4 at 1.26 a resolution Phyre2 PDB 1pem chain A Region: 2 - 38 Aligned: 36 Modelled: 37 Confidence: 22.9% Identity: 19% PDB header:oxidoreductase Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase 2 alpha PDBTitle: ribonucleotide reductase protein r1e from salmonella2 typhimurium Phyre2 PDB 1iuj chain A Region: 3 - 81 Aligned: 63 Modelled: 63 Confidence: 21.9% Identity: 16% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: PG130-like Phyre2 PDB 1edq chain A domain 1 Region: 48 - 73 Aligned: 26 Modelled: 26 Confidence: 21.1% Identity: 27% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: E-set domains of sugar-utilizing enzymes Phyre2 PDB 1peq chain A domain 2 Region: 4 - 38 Aligned: 34 Modelled: 35 Confidence: 20.6% Identity: 21% Fold: PFL-like glycyl radical enzymes Superfamily: PFL-like glycyl radical enzymes Family: R1 subunit of ribonucleotide reductase, C-terminal domain Phyre2 PDB 1xbw chain A Region: 1 - 81 Aligned: 65 Modelled: 81 Confidence: 19.4% Identity: 17% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: PG130-like Phyre2 PDB 3chg chain B Region: 21 - 89 Aligned: 68 Modelled: 69 Confidence: 17.5% Identity: 9% PDB header:ligand binding protein Chain: B: PDB Molecule:glycine betaine-binding protein; PDBTitle: the compatible solute-binding protein opuac from bacillus2 subtilis in complex with dmsa Phyre2 1 d2okqa1 2 c2okqB_ 3 d1vqsa_ 4 d1vqya1 5 d2fiua1 6 c3lo3E_ 7 c2wghA_ 8 c3nfqA_ 9 c2cvuA_ 10 c3hnfA_ 11 c2xpnA_ 12 c3dcaC_ 13 c3bm7A_ 14 c2rilA_ 15 c1pemA_ 16 d1iuja_ 17 d1edqa1 18 d1peqa2 19 d1xbwa_ 20 c3chgB_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49

Detailed template information

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

1 d2okqa1 100.0 100 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:YbaA-like 2 c2okqB_ 100.0 100 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ybaa; PDBTitle: crystal structure of unknown conserved ybaa protein from2 shigella flexneri 3 d1vqsa_ 87.4 19 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:NIPSNAP 4 d1vqya1 86.1 19 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:NIPSNAP 5 d2fiua1 80.5 23 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:Atu0297-like 6 c3lo3E_ 75.2 18 PDB header:structure genomics, unknown function Chain: E: PDB Molecule:uncharacterized conserved protein; PDBTitle: the crystal structure of a conserved functionally unknown2 protein from colwellia psychrerythraea 34h. 7 c2wghA_ 53.4 14 PDB header:oxidoreductase Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large PDBTitle: human ribonucleotide reductase r1 subunit (rrm1) in complex2 with datp and mg. 8 c3nfqA_ 52.2 25 PDB header:transcription Chain: A: PDB Molecule:transcription factor iws1; PDBTitle: crystal structure of the conserved central domain of yeast spn1/iws1 9 c2cvuA_ 51.4 19 PDB header:oxidoreductase Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large chain PDBTitle: structures of yeast ribonucleotide reductase i 10 c3hnfA_ 45.2 14 PDB header:oxidoreductase Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large subunit; PDBTitle: crystal structure of human ribonucleotide reductase 1 bound to the2 effectors ttp and datp 11 c2xpnA_ 44.7 18 PDB header:transcription Chain: A: PDB Molecule:iws1; PDBTitle: crystal structure of a spt6-iws1(spn1) complex from2 encephalitozoon cuniculi, form i 12 c3dcaC_ 33.2 19 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:rpa0582; PDBTitle: crystal structure of the rpa0582- protein of unknown2 function from rhodopseudomonas palustris- a structural3 genomics target 13 c3bm7A_ 31.0 21 PDB header:oxidoreductase Chain: A: PDB Molecule:protein of unknown function with ferredoxin-like fold; PDBTitle: crystal structure of a putative antibiotic biosynthesis monooxygenase2 (cc_2132) from caulobacter crescentus cb15 at 1.35 a resolution 14 c2rilA_ 29.9 22 PDB header:oxidoreductase Chain: A: PDB Molecule:antibiotic biosynthesis monooxygenase; PDBTitle: crystal structure of a putative monooxygenase (yp_001095275.1) from2 shewanella loihica pv-4 at 1.26 a resolution 15 c1pemA_ 22.9 19 PDB header:oxidoreductase Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase 2 alpha PDBTitle: ribonucleotide reductase protein r1e from salmonella2 typhimurium 16 d1iuja_ 21.9 16 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:PG130-like 17 d1edqa1 21.1 27 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:E-set domains of sugar-utilizing enzymes 18 d1peqa2 20.6 21 Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:R1 subunit of ribonucleotide reductase, C-terminal domain 19 d1xbwa_ 19.4 17 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:PG130-like 20 c3chgB_ 17.5 9 PDB header:ligand binding protein Chain: B: PDB Molecule:glycine betaine-binding protein; PDBTitle: the compatible solute-binding protein opuac from bacillus2 subtilis in complex with dmsa 21 c2qlxA_ not modelled 17.3 21 PDB header:isomerase Chain: A: PDB Molecule:l-rhamnose mutarotase; PDBTitle: crystal structure of rhamnose mutarotase rhau of rhizobium2 leguminosarum in complex with l-rhamnose 22 c2qlwA_ not modelled 17.2 21 PDB header:isomerase Chain: A: PDB Molecule:rhau; PDBTitle: crystal structure of rhamnose mutarotase rhau of rhizobium2 leguminosarum 23 d2k8ea1 not modelled 16.6 27 Fold:YegP-like Superfamily:YegP-like Family:YegP-like 24 d1rlra2 not modelled 16.2 9 Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:R1 subunit of ribonucleotide reductase, C-terminal domain 25 d2k49a2 not modelled 15.9 22 Fold:YegP-like Superfamily:YegP-like Family:YegP-like 26 d1iwpa_ not modelled 14.3 39 Fold:TIM beta/alpha-barrel Superfamily:Cobalamin (vitamin B12)-dependent enzymes Family:Diol dehydratase, alpha subunit 27 d1x4ha1 not modelled 12.5 9 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 28 d1fnxh2 not modelled 12.5 14 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 29 d2ix0a1 not modelled 12.4 22 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 30 d1imta2 not modelled 11.7 56 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Colipase-like Family:Colipase-like 31 d2qtva2 not modelled 11.1 50 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:beta-sandwich domain of Sec23/24 Family:beta-sandwich domain of Sec23/24 32 c3r1rB_ not modelled 10.6 8 PDB header:complex (oxidoreductase/peptide) Chain: B: PDB Molecule:ribonucleotide reductase r1 protein; PDBTitle: ribonucleotide reductase r1 protein with amppnp occupying2 the activity site from escherichia coli 33 d3bida1 not modelled 9.8 28 Fold:YegP-like Superfamily:YegP-like Family:YegP-like 34 d2omoa1 not modelled 9.4 19 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:PA3566-like 35 d1eexa_ not modelled 9.3 35 Fold:TIM beta/alpha-barrel Superfamily:Cobalamin (vitamin B12)-dependent enzymes Family:Diol dehydratase, alpha subunit 36 c1xjeA_ not modelled 9.3 25 PDB header:oxidoreductase Chain: A: PDB Molecule:ribonucleotide reductase, b12-dependent; PDBTitle: structural mechanism of allosteric substrate specificity in a2 ribonucleotide reductase: dttp-gdp complex 37 c3gh7A_ not modelled 8.8 13 PDB header:hydrolase Chain: A: PDB Molecule:beta-hexosaminidase; PDBTitle: crystal structure of beta-hexosaminidase from paenibacillus2 sp. ts12 in complex with galnac 38 d2k7ia1 not modelled 8.1 26 Fold:YegP-like Superfamily:YegP-like Family:YegP-like 39 c2k7iB_ not modelled 8.1 26 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:upf0339 protein atu0232; PDBTitle: solution nmr structure of protein atu0232 from agrobacterium2 tumefaciens. northeast structural genomics consortium (nesg) target3 att3. ontario center for structural proteomics target atc0223. 40 d2zdpa1 not modelled 7.4 8 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:PG130-like 41 c3p6yD_ not modelled 7.4 13 PDB header:rna binding protein/rna Chain: D: PDB Molecule:cleavage and polyadenylation specificity factor subunit 6; PDBTitle: cf im25-cf im68-uguaa complex 42 c2i38A_ not modelled 7.1 26 PDB header:rna binding protein/chimera Chain: A: PDB Molecule:fusion protein consists of immunoglobin g- PDBTitle: solution structure of the rrm of srp20 43 c2kdbA_ not modelled 6.6 19 PDB header:protein binding Chain: A: PDB Molecule:homocysteine-responsive endoplasmic reticulum- PDBTitle: solution structure of human ubiquitin-like domain of2 herpud2_9_85, northeast structural genomics consortium3 (nesg) target ht53a 44 c2k49A_ not modelled 6.6 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0339 protein so_3888; PDBTitle: solution nmr structure of upf0339 protein so3888 from shewanella2 oneidensis. northeast structural genomics consortium target sor190 45 c2f3jA_ not modelled 6.5 17 PDB header:transport protein Chain: A: PDB Molecule:rna and export factor binding protein 2; PDBTitle: the solution structure of the ref2-i mrna export factor2 (residues 1-155). 46 c1ylhA_ not modelled 5.6 14 PDB header:lyase Chain: A: PDB Molecule:phosphoenolpyruvate carboxykinase; PDBTitle: crystal structure of phosphoenolpyruvate carboxykinase from2 actinobaccilus succinogenes in complex with manganese and3 pyruvate 47 d1v3va1 not modelled 5.5 25 Fold:GroES-like Superfamily:GroES-like Family:Alcohol dehydrogenase-like, N-terminal domain 48 d1tz0a_ not modelled 5.3 24 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:PG130-like 49 c2omoC_ not modelled 5.3 19 PDB header:oxidoreductase Chain: C: PDB Molecule:duf176; PDBTitle: putative antibiotic biosynthesis monooxygenase from nitrosomonas2 europaea

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