Secondary structure and disorder prediction

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Sequence		M	G	R	I	L	L	D	L	S	N	E	V	I	K	Q	L	D	D	L	E	V	Q	R	N	L	P	R	A	D	L	L	R	E	A	V	D	Q	Y	L	I	N	Q	S	Q	T	A	R	T	S	V	P	G	I	W	Q	G	C	E	E	D
Secondary structure
SS confidence
Disorder		?	?	?	?	?		?														?	?	?	?	?	?																	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.
Sequence		G	V	E	Y	Q	R	K	L	R	E	E	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 2k5j chain B Region: 1 - 72 Aligned: 72 Modelled: 72 Confidence: 100.0% Identity: 100% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein yiif; PDBTitle: solution structure of protein yiif from shigella flexneri2 serotype 5b (strain 8401) . northeast structural genomics3 consortium target sft1 Phyre2 PDB 2bj3 chain D Region: 1 - 45 Aligned: 45 Modelled: 45 Confidence: 98.1% Identity: 11% PDB header:transcription Chain: D: PDB Molecule:nickel responsive regulator; PDBTitle: nikr-apo Phyre2 PDB 2bj7 chain A domain 1 Region: 1 - 43 Aligned: 43 Modelled: 43 Confidence: 98.1% Identity: 12% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 1q5v chain B Region: 1 - 48 Aligned: 48 Modelled: 48 Confidence: 98.0% Identity: 21% PDB header:transcription Chain: B: PDB Molecule:nickel responsive regulator; PDBTitle: apo-nikr Phyre2 PDB 2ca9 chain B Region: 1 - 44 Aligned: 44 Modelled: 44 Confidence: 98.0% Identity: 18% PDB header:transcriptional regulation Chain: B: PDB Molecule:putative nickel-responsive regulator; PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation Phyre2 PDB 2hza chain A domain 1 Region: 3 - 42 Aligned: 40 Modelled: 40 Confidence: 97.3% Identity: 23% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2hza chain B domain 1 Region: 3 - 42 Aligned: 40 Modelled: 40 Confidence: 97.1% Identity: 23% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2cpg chain A Region: 3 - 42 Aligned: 40 Modelled: 40 Confidence: 95.0% Identity: 23% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2rbf chain B Region: 4 - 41 Aligned: 38 Modelled: 38 Confidence: 94.4% Identity: 13% PDB header:oxidoreductase/dna Chain: B: PDB Molecule:bifunctional protein puta; PDBTitle: structure of the ribbon-helix-helix domain of escherichia coli puta2 (puta52) complexed with operator dna (o2) Phyre2 PDB 2k9i chain B Region: 2 - 43 Aligned: 42 Modelled: 42 Confidence: 93.5% Identity: 24% PDB header:dna binding protein Chain: B: PDB Molecule:plasmid prn1, complete sequence; PDBTitle: nmr structure of plasmid copy control protein orf56 from2 sulfolobus islandicus Phyre2 PDB 3h87 chain D Region: 7 - 72 Aligned: 65 Modelled: 66 Confidence: 91.5% Identity: 20% PDB header:toxin/antitoxin Chain: D: PDB Molecule:putative uncharacterized protein; PDBTitle: rv0301 rv0300 toxin antitoxin complex from mycobacterium tuberculosis Phyre2 PDB 2an7 chain A Region: 1 - 26 Aligned: 26 Modelled: 26 Confidence: 88.7% Identity: 19% PDB header:dna binding protein Chain: A: PDB Molecule:protein pard; PDBTitle: solution structure of the bacterial antidote pard Phyre2 PDB 2kel chain B Region: 6 - 41 Aligned: 36 Modelled: 36 Confidence: 86.3% Identity: 19% PDB header:transcription repressor Chain: B: PDB Molecule:uncharacterized protein 56b; PDBTitle: structure of the transcription regulator svtr from the2 hyperthermophilic archaeal virus sirv1 Phyre2 PDB 2ay0 chain A domain 1 Region: 2 - 41 Aligned: 40 Modelled: 40 Confidence: 79.0% Identity: 13% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: PutA pre-N-terminal region-like Phyre2 PDB 1p94 chain A Region: 3 - 42 Aligned: 40 Modelled: 40 Confidence: 78.0% Identity: 15% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2k29 chain A Region: 1 - 45 Aligned: 45 Modelled: 45 Confidence: 76.5% Identity: 18% PDB header:transcription Chain: A: PDB Molecule:antitoxin relb; PDBTitle: structure of the dbd domain of e. coli antitoxin relb Phyre2 PDB 3kxe chain D Region: 4 - 41 Aligned: 38 Modelled: 38 Confidence: 66.5% Identity: 11% PDB header:protein binding Chain: D: PDB Molecule:antitoxin protein pard-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex Phyre2 PDB 2bsq chain E domain 1 Region: 4 - 60 Aligned: 57 Modelled: 57 Confidence: 64.5% Identity: 14% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: Trafficking protein A-like Phyre2 PDB 1mnt chain A Region: 4 - 44 Aligned: 41 Modelled: 41 Confidence: 48.7% Identity: 17% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: Arc/Mnt-like phage repressors Phyre2 PDB 2q2k chain A Region: 14 - 40 Aligned: 27 Modelled: 27 Confidence: 32.9% Identity: 26% PDB header:dna binding protein/dna Chain: A: PDB Molecule:hypothetical protein; PDBTitle: structure of nucleic-acid binding protein Phyre2 1 c2k5jB_ 2 c2bj3D_ 3 d2bj7a1 4 c1q5vB_ 5 c2ca9B_ 6 d2hzaa1 7 d2hzab1 8 d2cpga_ 9 c2rbfB_ 10 c2k9iB_ 11 c3h87D_ 12 c2an7A_ 13 c2kelB_ 14 d2ay0a1 15 d1p94a_ 16 c2k29A_ 17 c3kxeD_ 18 d2bsqe1 19 d1mnta_ 20 c2q2kA_ 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 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75

Detailed template information

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

1 c2k5jB_ 100.0 100 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein yiif; PDBTitle: solution structure of protein yiif from shigella flexneri2 serotype 5b (strain 8401) . northeast structural genomics3 consortium target sft1 2 c2bj3D_ 98.1 11 PDB header:transcription Chain: D: PDB Molecule:nickel responsive regulator; PDBTitle: nikr-apo 3 d2bj7a1 98.1 12 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 4 c1q5vB_ 98.0 21 PDB header:transcription Chain: B: PDB Molecule:nickel responsive regulator; PDBTitle: apo-nikr 5 c2ca9B_ 98.0 18 PDB header:transcriptional regulation Chain: B: PDB Molecule:putative nickel-responsive regulator; PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation 6 d2hzaa1 97.3 23 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 7 d2hzab1 97.1 23 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 8 d2cpga_ 95.0 23 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 9 c2rbfB_ 94.4 13 PDB header:oxidoreductase/dna Chain: B: PDB Molecule:bifunctional protein puta; PDBTitle: structure of the ribbon-helix-helix domain of escherichia coli puta2 (puta52) complexed with operator dna (o2) 10 c2k9iB_ 93.5 24 PDB header:dna binding protein Chain: B: PDB Molecule:plasmid prn1, complete sequence; PDBTitle: nmr structure of plasmid copy control protein orf56 from2 sulfolobus islandicus 11 c3h87D_ 91.5 20 PDB header:toxin/antitoxin Chain: D: PDB Molecule:putative uncharacterized protein; PDBTitle: rv0301 rv0300 toxin antitoxin complex from mycobacterium tuberculosis 12 c2an7A_ 88.7 19 PDB header:dna binding protein Chain: A: PDB Molecule:protein pard; PDBTitle: solution structure of the bacterial antidote pard 13 c2kelB_ 86.3 19 PDB header:transcription repressor Chain: B: PDB Molecule:uncharacterized protein 56b; PDBTitle: structure of the transcription regulator svtr from the2 hyperthermophilic archaeal virus sirv1 14 d2ay0a1 79.0 13 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:PutA pre-N-terminal region-like 15 d1p94a_ 78.0 15 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 16 c2k29A_ 76.5 18 PDB header:transcription Chain: A: PDB Molecule:antitoxin relb; PDBTitle: structure of the dbd domain of e. coli antitoxin relb 17 c3kxeD_ 66.5 11 PDB header:protein binding Chain: D: PDB Molecule:antitoxin protein pard-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex 18 d2bsqe1 64.5 14 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Trafficking protein A-like 19 d1mnta_ 48.7 17 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Arc/Mnt-like phage repressors 20 c2q2kA_ 32.9 26 PDB header:dna binding protein/dna Chain: A: PDB Molecule:hypothetical protein; PDBTitle: structure of nucleic-acid binding protein 21 c1kcfB_ not modelled 28.1 33 PDB header:hydrolase Chain: B: PDB Molecule:hypothetical 30.2 kd protein c25g10.02 in PDBTitle: crystal structure of the yeast mitochondrial holliday2 junction resolvase, ydc2 22 d1y9ba1 not modelled 24.8 12 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:VCA0319-like 23 c3c5yD_ not modelled 21.3 9 PDB header:isomerase Chain: D: PDB Molecule:ribose/galactose isomerase; PDBTitle: crystal structure of a putative ribose 5-phosphate isomerase2 (saro_3514) from novosphingobium aromaticivorans dsm at 1.81 a3 resolution 24 c2qhoF_ not modelled 19.9 28 PDB header:protein binding/ligase Chain: F: PDB Molecule:e3 ubiquitin-protein ligase edd1; PDBTitle: crystal structure of the uba domain from edd ubiquitin2 ligase in complex with ubiquitin 25 c2hwyB_ not modelled 18.6 27 PDB header:rna binding protein Chain: B: PDB Molecule:protein smg5; PDBTitle: structure of pin domain of human smg5. 26 c2kkeA_ not modelled 18.3 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of a dimeric protein of unknown2 function from methanobacterium thermoautotrophicum,3 northeast structural genomics consortium target tr5 27 c2ppwA_ not modelled 15.6 8 PDB header:isomerase Chain: A: PDB Molecule:conserved domain protein; PDBTitle: the crystal structure of uncharacterized ribose 5-phosphate isomerase2 rpib from streptococcus pneumoniae 28 c1ny9A_ not modelled 14.8 13 PDB header:transcription Chain: A: PDB Molecule:transcriptional activator tipa-s; PDBTitle: antibiotic binding domain of a tipa-class multidrug2 resistance transcriptional regulator 29 d1ny9a_ not modelled 14.8 13 Fold:Antibiotic binding domain of TipA-like multidrug resistance regulators Superfamily:Antibiotic binding domain of TipA-like multidrug resistance regulators Family:Antibiotic binding domain of TipA-like multidrug resistance regulators 30 c1yxeA_ not modelled 14.2 10 PDB header:immune system Chain: A: PDB Molecule:apical membrane antigen 1; PDBTitle: structure and inter-domain interactions of domain ii from the blood2 stage malarial protein, apical membrane antigen 1 31 c1u9pA_ not modelled 12.8 10 PDB header:unknown function Chain: A: PDB Molecule:parc; PDBTitle: permuted single-chain arc 32 c2xv9A_ not modelled 11.3 17 PDB header:lipid binding protein Chain: A: PDB Molecule:aba-1a1 repeat unit; PDBTitle: the solution structure of aba-1a saturated with oleic acid 33 d2proc1 not modelled 10.7 42 Fold:Alpha-lytic protease prodomain-like Superfamily:Alpha-lytic protease prodomain Family:Alpha-lytic protease prodomain 34 c3iwfA_ not modelled 10.7 12 PDB header:transcription regulator Chain: A: PDB Molecule:transcription regulator rpir family; PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a 35 c3onoA_ not modelled 10.3 5 PDB header:isomerase Chain: A: PDB Molecule:ribose/galactose isomerase; PDBTitle: crystal structure of ribose-5-phosphate isomerase lacab_rpib from2 vibrio parahaemolyticus 36 d2o3fa1 not modelled 9.9 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:RpiR-like 37 c2o3fC_ not modelled 9.9 18 PDB header:transcription Chain: C: PDB Molecule:putative hth-type transcriptional regulator ybbh; PDBTitle: structural genomics, the crystal structure of the n-2 terminal domain of the putative transcriptional regulator3 ybbh from bacillus subtilis subsp. subtilis str. 168. 38 c3oeoD_ not modelled 9.8 12 PDB header:signaling protein Chain: D: PDB Molecule:spheroplast protein y; PDBTitle: the crystal structure e. coli spy 39 c3kk4B_ not modelled 9.5 10 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein bp1543; PDBTitle: uncharacterized protein bp1543 from bordetella pertussis tohama i 40 d2je6b2 not modelled 9.1 25 Fold:Ribonuclease PH domain 2-like Superfamily:Ribonuclease PH domain 2-like Family:Ribonuclease PH domain 2-like 41 c3o39A_ not modelled 9.0 12 PDB header:chaperone Chain: A: PDB Molecule:periplasmic protein related to spheroblast formation; PDBTitle: crystal structure of spy 42 d1uxca_ not modelled 8.9 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 43 d2phcb1 not modelled 8.8 12 Fold:Cyclophilin-like Superfamily:Cyclophilin-like Family:PH0987 C-terminal domain-like 44 d2qklb1 not modelled 8.5 28 Fold:Dcp2 domain-like Superfamily:Dcp2 domain-like Family:Dcp2 box A domain 45 d1znda1 not modelled 8.4 23 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 46 d1to0a_ not modelled 8.3 10 Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like 47 d1gm6a_ not modelled 8.0 13 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 48 d1l5aa2 not modelled 7.5 13 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:NRPS condensation domain (amide synthase) 49 c2l8nA_ not modelled 7.5 18 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional repressor cytr; PDBTitle: nmr structure of the cytidine repressor dna binding domain in presence2 of operator half-site dna 50 d2c2vv1 not modelled 7.3 17 Fold:RING/U-box Superfamily:RING/U-box Family:U-box 51 d1q9ja2 not modelled 7.2 16 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:NRPS condensation domain (amide synthase) 52 c2lcvA_ not modelled 7.0 18 PDB header:transcription regulator Chain: A: PDB Molecule:hth-type transcriptional repressor cytr; PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation 53 c2zp2B_ not modelled 6.9 12 PDB header:transferase inhibitor Chain: B: PDB Molecule:kinase a inhibitor; PDBTitle: c-terminal domain of kipi from bacillus subtilis 54 c2e4jA_ not modelled 6.9 16 PDB header:isomerase Chain: A: PDB Molecule:prostaglandin-h2 d-isomerase; PDBTitle: solution structure of mouse lipocalin-type prostaglandin d2 synthase 55 c3epvB_ not modelled 6.9 13 PDB header:metal binding protein Chain: B: PDB Molecule:nickel and cobalt resistance protein cnrr; PDBTitle: x-ray structure of the metal-sensor cnrx in both the apo- and copper-2 bound forms 56 d1cjya2 not modelled 6.9 23 Fold:FabD/lysophospholipase-like Superfamily:FabD/lysophospholipase-like Family:Lysophospholipase 57 c2wteB_ not modelled 6.8 26 PDB header:antiviral protein Chain: B: PDB Molecule:csa3; PDBTitle: the structure of the crispr-associated protein, csa3, from2 sulfolobus solfataricus at 1.8 angstrom resolution. 58 c3qzcA_ not modelled 6.8 14 PDB header:signaling protein Chain: A: PDB Molecule:periplasmic protein cpxp; PDBTitle: structure of the periplasmic stress response protein cpxp 59 c4a1qB_ not modelled 6.4 26 PDB header:viral protein Chain: B: PDB Molecule:orf e73; PDBTitle: solution structure of e73 protein from sulfolobus spindle-2 shaped virus ragged hills, a hyperthermophilic3 crenarchaeal virus from yellowstone national park 60 c2qkmF_ not modelled 6.4 23 PDB header:hydrolase Chain: F: PDB Molecule:spac19a8.12 protein; PDBTitle: the crystal structure of fission yeast mrna decapping enzyme dcp1-dcp22 complex 61 d2obpa1 not modelled 5.9 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ReutB4095-like 62 d1y0ya2 not modelled 5.9 12 Fold:Phosphorylase/hydrolase-like Superfamily:Zn-dependent exopeptidases Family:Bacterial dinuclear zinc exopeptidases 63 c2kp6A_ not modelled 5.8 8 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of protein cv0237 from2 chromobacterium violaceum. northeast structural genomics3 consortium (nesg) target cvt1 64 d1ns5a_ not modelled 5.8 17 Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like 65 d1lcda_ not modelled 5.8 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 66 d1uxda_ not modelled 5.7 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 67 d2hsga1 not modelled 5.7 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 68 d1qpza1 not modelled 5.7 12 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 69 d2nn6d2 not modelled 5.5 13 Fold:Ribonuclease PH domain 2-like Superfamily:Ribonuclease PH domain 2-like Family:Ribonuclease PH domain 2-like 70 c2xstA_ not modelled 5.5 23 PDB header:transport protein Chain: A: PDB Molecule:lipocalin 15; PDBTitle: crystal structure of the human lipocalin 15 71 c3by0B_ not modelled 5.4 16 PDB header:ligand binding protein Chain: B: PDB Molecule:neutrophil gelatinase-associated lipocalin; PDBTitle: crystal structure of siderocalin (ngal, lipocalin 2) w79a-r81a2 complexed with ferric enterobactin 72 c3p3vB_ not modelled 5.2 10 PDB header:transferase Chain: B: PDB Molecule:pts system, n-acetylgalactosamine-specific iib component; PDBTitle: crystal structure of a pts dependent n-acetyl-galactosamine-iib2 component (agav, spy_0631) from streptococcus pyogenes at 1.65 a3 resolution 73 d1t1ha_ not modelled 5.2 8 Fold:RING/U-box Superfamily:RING/U-box Family:U-box 74 c3i8oA_ not modelled 5.1 10 PDB header:rna binding protein Chain: A: PDB Molecule:kh domain-containing protein mj1533; PDBTitle: a domain of a functionally unknown protein from2 methanocaldococcus jannaschii dsm 2661. 75 d1cuka1 not modelled 5.1 18 Fold:RuvA C-terminal domain-like Superfamily:DNA helicase RuvA subunit, C-terminal domain Family:DNA helicase RuvA subunit, 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

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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