Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	V	T	T	S	D	V	V	M	C	Q	M	R	R	S	D	V	Q	G	G	Y	R	V	Y	G	S	W	M	A	E	N	V	Q	D	Q	V	S	I	L	N	Q	K	L	S	E	F	A	P	S	M	P	H	A	V	R	S	D	V	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?																											?	?	?																					?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.
Sequence		N	N	R	L	Q	N	L	H	L	H	A	H	H	F	L	I	R	R	H	Q	L	I	T	H	L	N	P	H	L	H	R	N
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 3nkh chain B Region: 7 - 42 Aligned: 36 Modelled: 36 Confidence: 94.2% Identity: 17% PDB header:recombination Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of integrase from mrsa strain staphylococcus aureus Phyre2 PDB 1ma7 chain A Region: 7 - 41 Aligned: 34 Modelled: 35 Confidence: 72.7% Identity: 15% PDB header:hydrolase, ligase/dna Chain: A: PDB Molecule:cre recombinase; PDBTitle: crystal structure of cre site-specific recombinase2 complexed with a mutant dna substrate, loxp-a8/t27 Phyre2 PDB 1f44 chain A domain 2 Region: 7 - 41 Aligned: 34 Modelled: 35 Confidence: 65.5% Identity: 12% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 2a3v chain A Region: 7 - 25 Aligned: 18 Modelled: 19 Confidence: 38.4% Identity: 28% PDB header:recombination Chain: A: PDB Molecule:site-specific recombinase inti4; PDBTitle: structural basis for broad dna-specificity in integron2 recombination Phyre2 PDB 1crx chain A Region: 7 - 41 Aligned: 34 Modelled: 35 Confidence: 37.3% Identity: 15% PDB header:replication/dna Chain: A: PDB Molecule:cre recombinase; PDBTitle: cre recombinase/dna complex reaction intermediate i Phyre2 PDB 1aih chain A Region: 7 - 39 Aligned: 32 Modelled: 33 Confidence: 35.4% Identity: 13% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 1wii chain A Region: 23 - 31 Aligned: 9 Modelled: 9 Confidence: 20.8% Identity: 33% Fold: Rubredoxin-like Superfamily: Zinc beta-ribbon Family: Putative zinc binding domain Phyre2 PDB 1q46 chain A domain 1 Region: 3 - 24 Aligned: 22 Modelled: 22 Confidence: 13.8% Identity: 14% Fold: SAM domain-like Superfamily: eIF2alpha middle domain-like Family: eIF2alpha middle domain-like Phyre2 PDB 1z1b chain A Region: 7 - 21 Aligned: 15 Modelled: 15 Confidence: 12.4% Identity: 0% PDB header:dna binding protein/dna Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of a lambda integrase dimer bound to a2 coc' core site Phyre2 PDB 1v54 chain L Region: 74 - 81 Aligned: 8 Modelled: 8 Confidence: 10.4% Identity: 75% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Family: Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Phyre2 PDB 1a0p chain A Region: 7 - 22 Aligned: 16 Modelled: 16 Confidence: 10.2% Identity: 19% PDB header:dna recombination Chain: A: PDB Molecule:site-specific recombinase xerd; PDBTitle: site-specific recombinase, xerd Phyre2 PDB 1p7d chain A Region: 7 - 20 Aligned: 14 Modelled: 14 Confidence: 9.6% Identity: 0% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 2y69 chain Y Region: 74 - 81 Aligned: 8 Modelled: 8 Confidence: 9.5% Identity: 75% PDB header:electron transport Chain: Y: PDB Molecule:cytochrome c oxidase subunit 7c; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1gxh chain A Region: 38 - 60 Aligned: 23 Modelled: 23 Confidence: 8.9% Identity: 26% Fold: Acyl carrier protein-like Superfamily: Colicin E immunity proteins Family: Colicin E immunity proteins Phyre2 PDB 1kzv chain A Region: 15 - 26 Aligned: 12 Modelled: 12 Confidence: 8.4% Identity: 33% PDB header:viral protein Chain: A: PDB Molecule:vpr protein; PDBTitle: structure of human immunodeficiency virus type 1 vpr(34-51)2 peptide in chloroform methanol Phyre2 PDB 1kzt chain A Region: 15 - 26 Aligned: 12 Modelled: 12 Confidence: 8.4% Identity: 33% PDB header:viral protein Chain: A: PDB Molecule:vpr protein; PDBTitle: structure of human immunodeficiency virus type 1 vpr(34-51)2 peptide in dpc micelle containing aqueous solution Phyre2 PDB 1kzs chain A Region: 15 - 26 Aligned: 12 Modelled: 12 Confidence: 8.4% Identity: 33% PDB header:viral protein Chain: A: PDB Molecule:vpr protein; PDBTitle: structure of human immunodeficiency virus type 1 vpr(34-51)2 peptide in aqueous tfe solution Phyre2 PDB 1ytr chain A Region: 12 - 28 Aligned: 17 Modelled: 17 Confidence: 7.2% Identity: 18% PDB header:antibiotic Chain: A: PDB Molecule:bacteriocin plantaricin a; PDBTitle: nmr structure of plantaricin a in dpc micelles, 202 structures Phyre2 PDB 2hi3 chain A domain 1 Region: 33 - 64 Aligned: 31 Modelled: 32 Confidence: 7.1% Identity: 23% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Homeodomain Phyre2 PDB 2k8j chain X Region: 22 - 28 Aligned: 7 Modelled: 7 Confidence: 6.7% Identity: 57% PDB header:viral protein Chain: X: PDB Molecule:p7tm2; PDBTitle: solution structure of hcv p7 tm2 Phyre2 1 c3nkhB_ 2 c1ma7A_ 3 d1f44a2 4 c2a3vA_ 5 c1crxA_ 6 d1aiha_ 7 d1wiia_ 8 d1q46a1 9 c1z1bA_ 10 d1v54l_ 11 c1a0pA_ 12 d1p7da_ 13 c2y69Y_ 14 d1gxha_ 15 c1kzvA_ 16 c1kztA_ 17 c1kzsA_ 18 c1ytrA_ 19 d2hi3a1 20 c2k8jX_ 21 22 23 24 25 26 27 28 29 30 31 32 33

Detailed template information

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

1 c3nkhB_ 94.2 17 PDB header:recombination Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of integrase from mrsa strain staphylococcus aureus 2 c1ma7A_ 72.7 15 PDB header:hydrolase, ligase/dna Chain: A: PDB Molecule:cre recombinase; PDBTitle: crystal structure of cre site-specific recombinase2 complexed with a mutant dna substrate, loxp-a8/t27 3 d1f44a2 65.5 12 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 4 c2a3vA_ 38.4 28 PDB header:recombination Chain: A: PDB Molecule:site-specific recombinase inti4; PDBTitle: structural basis for broad dna-specificity in integron2 recombination 5 c1crxA_ 37.3 15 PDB header:replication/dna Chain: A: PDB Molecule:cre recombinase; PDBTitle: cre recombinase/dna complex reaction intermediate i 6 d1aiha_ 35.4 13 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 7 d1wiia_ 20.8 33 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Putative zinc binding domain 8 d1q46a1 13.8 14 Fold:SAM domain-like Superfamily:eIF2alpha middle domain-like Family:eIF2alpha middle domain-like 9 c1z1bA_ 12.4 0 PDB header:dna binding protein/dna Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of a lambda integrase dimer bound to a2 coc' core site 10 d1v54l_ 10.4 75 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Family:Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) 11 c1a0pA_ 10.2 19 PDB header:dna recombination Chain: A: PDB Molecule:site-specific recombinase xerd; PDBTitle: site-specific recombinase, xerd 12 d1p7da_ 9.6 0 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 13 c2y69Y_ 9.5 75 PDB header:electron transport Chain: Y: PDB Molecule:cytochrome c oxidase subunit 7c; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 14 d1gxha_ 8.9 26 Fold:Acyl carrier protein-like Superfamily:Colicin E immunity proteins Family:Colicin E immunity proteins 15 c1kzvA_ 8.4 33 PDB header:viral protein Chain: A: PDB Molecule:vpr protein; PDBTitle: structure of human immunodeficiency virus type 1 vpr(34-51)2 peptide in chloroform methanol 16 c1kztA_ 8.4 33 PDB header:viral protein Chain: A: PDB Molecule:vpr protein; PDBTitle: structure of human immunodeficiency virus type 1 vpr(34-51)2 peptide in dpc micelle containing aqueous solution 17 c1kzsA_ 8.4 33 PDB header:viral protein Chain: A: PDB Molecule:vpr protein; PDBTitle: structure of human immunodeficiency virus type 1 vpr(34-51)2 peptide in aqueous tfe solution 18 c1ytrA_ 7.2 18 PDB header:antibiotic Chain: A: PDB Molecule:bacteriocin plantaricin a; PDBTitle: nmr structure of plantaricin a in dpc micelles, 202 structures 19 d2hi3a1 7.1 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 20 c2k8jX_ 6.7 57 PDB header:viral protein Chain: X: PDB Molecule:p7tm2; PDBTitle: solution structure of hcv p7 tm2 21 d2gy9s1 not modelled 6.6 46 Fold:Ribosomal protein S19 Superfamily:Ribosomal protein S19 Family:Ribosomal protein S19 22 d1uhsa_ not modelled 6.6 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 23 c2wl8D_ not modelled 6.5 15 PDB header:protein transport Chain: D: PDB Molecule:peroxisomal biogenesis factor 19; PDBTitle: x-ray crystal structure of pex19p 24 c1zd1B_ not modelled 6.0 10 PDB header:transferase Chain: B: PDB Molecule:sulfotransferase 4a1; PDBTitle: human sulfortransferase sult4a1 25 d1f15b_ not modelled 5.7 35 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Bromoviridae-like VP 26 c2wvmA_ not modelled 5.7 55 PDB header:transferase Chain: A: PDB Molecule:mannosyl-3-phosphoglycerate synthase; PDBTitle: h309a mutant of mannosyl-3-phosphoglycerate synthase from2 thermus thermophilus hb27 in complex with3 gdp-alpha-d-mannose and mg(ii) 27 d1f06a2 not modelled 5.6 29 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Dihydrodipicolinate reductase-like 28 c1f15C_ not modelled 5.6 35 PDB header:virus Chain: C: PDB Molecule:coat protein; PDBTitle: cucumber mosaic virus (strain fny) 29 c2l5gA_ not modelled 5.6 29 PDB header:transcription regulator Chain: A: PDB Molecule:g protein pathway suppressor 2; PDBTitle: co-ordinates and 1h, 13c and 15n chemical shift assignments for the2 complex of gps2 53-90 and smrt 167-207 30 d5csma_ not modelled 5.5 17 Fold:Chorismate mutase II Superfamily:Chorismate mutase II Family:Allosteric chorismate mutase 31 d1i94m_ not modelled 5.4 9 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Ribosomal protein S13 32 d2uubs1 not modelled 5.2 46 Fold:Ribosomal protein S19 Superfamily:Ribosomal protein S19 Family:Ribosomal protein S19 33 d1ayia_ not modelled 5.2 21 Fold:Acyl carrier protein-like Superfamily:Colicin E immunity proteins Family:Colicin E immunity proteins

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