Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	G	S	V	I	H	S	Q	S	A	V	M	V	P	A	V	Y	S	A	G	Q	P	A	S	L	P	V	A	I	D	Y	P	A	A	L	A	L	R	Q	M	S	M	V	H	D	E	L	P	K	Y	L	L	A	P	E	V	S	A	L
Secondary structure
SS confidence
Disorder		?	?										?											?	?	?	?				?	?		?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	H	Y	V	P	D	L	H	R	K	M	L	L	A	T	L	W	N	T	G	A	R	I	N	E	A	L	A	L	T	R	G	D	F	S	L	A	P	P	Y	P	F	V	Q	L	A	T	L	K	Q	R	T	E	K	A	A	R	T	A	G
Secondary structure
SS confidence
Disorder																																																			?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	M	P	A	G	Q	Q	T	H	R	L	V	P	L	S	D	S	W	Y	V	S	Q	L	Q	T	M	V	A	Q	L	K	I	P	M	E	R	R	N	R	R	T	G	R	T	E	K	A	R	I	W	E	V	T	D	R	T	V	R	T	W
Secondary structure
SS confidence
Disorder																																	?		?		?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	G	E	A	V	A	A	A	A	A	D	G	V	T	F	S	V	P	V	T	P	H	T	F	R	H	S	Y	A	M	H	M	L	Y	A	G	I	P	L	K	V	L	Q	S	L	M	G	H	K	S	I	S	S	T	E	V	Y	T	K	V
Secondary structure
SS confidence
Disorder													?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.
Sequence		F	A	L	D	V	A	A	R	H	R	V	Q	F	A	M	P	E	S	D	A	V	A	M	L	K	Q	L	S
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: 50 - 251 Aligned: 197 Modelled: 197 Confidence: 100.0% Identity: 17% PDB header:recombination Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of integrase from mrsa strain staphylococcus aureus Phyre2 PDB 1z1b chain A Region: 2 - 239 Aligned: 205 Modelled: 224 Confidence: 99.9% Identity: 16% 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 1a0p chain A domain 2 Region: 50 - 250 Aligned: 175 Modelled: 181 Confidence: 99.9% Identity: 29% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 1f44 chain A domain 2 Region: 52 - 239 Aligned: 176 Modelled: 188 Confidence: 99.9% Identity: 13% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 1p7d chain A Region: 2 - 243 Aligned: 209 Modelled: 226 Confidence: 99.9% Identity: 16% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 1aih chain A Region: 37 - 258 Aligned: 169 Modelled: 178 Confidence: 99.9% Identity: 17% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 1crx chain A Region: 4 - 244 Aligned: 225 Modelled: 228 Confidence: 99.9% Identity: 12% PDB header:replication/dna Chain: A: PDB Molecule:cre recombinase; PDBTitle: cre recombinase/dna complex reaction intermediate i Phyre2 PDB 1ma7 chain A Region: 4 - 244 Aligned: 227 Modelled: 228 Confidence: 99.9% Identity: 11% 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 1a0p chain A Region: 2 - 250 Aligned: 209 Modelled: 215 Confidence: 99.9% Identity: 23% PDB header:dna recombination Chain: A: PDB Molecule:site-specific recombinase xerd; PDBTitle: site-specific recombinase, xerd Phyre2 PDB 1ae9 chain A Region: 52 - 241 Aligned: 165 Modelled: 176 Confidence: 99.9% Identity: 18% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 2a3v chain A Region: 2 - 249 Aligned: 233 Modelled: 248 Confidence: 99.9% Identity: 15% PDB header:recombination Chain: A: PDB Molecule:site-specific recombinase inti4; PDBTitle: structural basis for broad dna-specificity in integron2 recombination Phyre2 PDB 5crx chain B domain 2 Region: 52 - 227 Aligned: 163 Modelled: 163 Confidence: 99.8% Identity: 12% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 2v6e chain B Region: 66 - 237 Aligned: 157 Modelled: 160 Confidence: 96.8% Identity: 13% PDB header:hydrolase Chain: B: PDB Molecule:protelemorase; PDBTitle: protelomerase telk complexed with substrate dna Phyre2 PDB 2f4q chain A Region: 70 - 268 Aligned: 164 Modelled: 179 Confidence: 95.4% Identity: 13% PDB header:isomerase Chain: A: PDB Molecule:type i topoisomerase, putative; PDBTitle: crystal structure of deinococcus radiodurans topoisomerase ib Phyre2 PDB 2khq chain A Region: 2 - 41 Aligned: 40 Modelled: 40 Confidence: 88.5% Identity: 5% PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: solution nmr structure of a phage integrase ssp19472 fragment 59-159 from staphylococcus saprophyticus,3 northeast structural genomics consortium target syr103b Phyre2 PDB 2h7f chain X Region: 70 - 267 Aligned: 156 Modelled: 181 Confidence: 87.8% Identity: 13% PDB header:isomerase/dna Chain: X: PDB Molecule:dna topoisomerase 1; PDBTitle: structure of variola topoisomerase covalently bound to dna Phyre2 PDB 2kob chain A Region: 4 - 44 Aligned: 41 Modelled: 41 Confidence: 86.4% Identity: 7% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of clolep_01837 (fragment 61-160)2 from clostridium leptum. northeast structural genomics3 consortium target qlr8a Phyre2 PDB 2kkp chain A Region: 2 - 40 Aligned: 39 Modelled: 39 Confidence: 86.1% Identity: 13% PDB header:dna binding protein Chain: A: PDB Molecule:phage integrase; PDBTitle: solution nmr structure of the phage integrase sam-like2 domain from moth 1796 from moorella thermoacetica.3 northeast structural genomics consortium target mtr39k4 (residues 64-171). Phyre2 PDB 2kiw chain A Region: 2 - 37 Aligned: 36 Modelled: 36 Confidence: 85.7% Identity: 17% PDB header:dna binding protein Chain: A: PDB Molecule:int protein; PDBTitle: solution nmr structure of the domain n-terminal to the2 integrase domain of sh1003 from staphylococcus3 haemolyticus. northeast structural genomics consortium4 target shr105f (64-166). Phyre2 PDB 2kd1 chain A Region: 3 - 44 Aligned: 42 Modelled: 42 Confidence: 83.4% Identity: 10% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:dna integration/recombination/invertion protein; PDBTitle: solution nmr structure of the integrase-like domain from2 bacillus cereus ordered locus bc_1272. northeast3 structural genomics consortium target bcr268f Phyre2 1 c3nkhB_ 2 c1z1bA_ 3 d1a0pa2 4 d1f44a2 5 d1p7da_ 6 d1aiha_ 7 c1crxA_ 8 c1ma7A_ 9 c1a0pA_ 10 d1ae9a_ 11 c2a3vA_ 12 d5crxb2 13 c2v6eB_ 14 c2f4qA_ 15 c2khqA_ 16 c2h7fX_ 17 c2kobA_ 18 c2kkpA_ 19 c2kiwA_ 20 c2kd1A_ 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 c3nkhB_ 100.0 17 PDB header:recombination Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of integrase from mrsa strain staphylococcus aureus 2 c1z1bA_ 99.9 16 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 3 d1a0pa2 99.9 29 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 4 d1f44a2 99.9 13 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 5 d1p7da_ 99.9 16 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 6 d1aiha_ 99.9 17 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 7 c1crxA_ 99.9 12 PDB header:replication/dna Chain: A: PDB Molecule:cre recombinase; PDBTitle: cre recombinase/dna complex reaction intermediate i 8 c1ma7A_ 99.9 11 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 9 c1a0pA_ 99.9 23 PDB header:dna recombination Chain: A: PDB Molecule:site-specific recombinase xerd; PDBTitle: site-specific recombinase, xerd 10 d1ae9a_ 99.9 18 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 11 c2a3vA_ 99.9 15 PDB header:recombination Chain: A: PDB Molecule:site-specific recombinase inti4; PDBTitle: structural basis for broad dna-specificity in integron2 recombination 12 d5crxb2 99.8 12 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 13 c2v6eB_ 96.8 13 PDB header:hydrolase Chain: B: PDB Molecule:protelemorase; PDBTitle: protelomerase telk complexed with substrate dna 14 c2f4qA_ 95.4 13 PDB header:isomerase Chain: A: PDB Molecule:type i topoisomerase, putative; PDBTitle: crystal structure of deinococcus radiodurans topoisomerase ib 15 c2khqA_ 88.5 5 PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: solution nmr structure of a phage integrase ssp19472 fragment 59-159 from staphylococcus saprophyticus,3 northeast structural genomics consortium target syr103b 16 c2h7fX_ 87.8 13 PDB header:isomerase/dna Chain: X: PDB Molecule:dna topoisomerase 1; PDBTitle: structure of variola topoisomerase covalently bound to dna 17 c2kobA_ 86.4 7 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of clolep_01837 (fragment 61-160)2 from clostridium leptum. northeast structural genomics3 consortium target qlr8a 18 c2kkpA_ 86.1 13 PDB header:dna binding protein Chain: A: PDB Molecule:phage integrase; PDBTitle: solution nmr structure of the phage integrase sam-like2 domain from moth 1796 from moorella thermoacetica.3 northeast structural genomics consortium target mtr39k4 (residues 64-171). 19 c2kiwA_ 85.7 17 PDB header:dna binding protein Chain: A: PDB Molecule:int protein; PDBTitle: solution nmr structure of the domain n-terminal to the2 integrase domain of sh1003 from staphylococcus3 haemolyticus. northeast structural genomics consortium4 target shr105f (64-166). 20 c2kd1A_ 83.4 10 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:dna integration/recombination/invertion protein; PDBTitle: solution nmr structure of the integrase-like domain from2 bacillus cereus ordered locus bc_1272. northeast3 structural genomics consortium target bcr268f 21 c2kj5A_ not modelled 71.6 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:phage integrase; PDBTitle: solution nmr structure of a domain from a putative phage2 integrase protein nmul_a0064 from nitrosospira multiformis,3 northeast structural genomics consortium target nmr46c 22 c1p4eB_ not modelled 69.5 12 PDB header:dna binding protein/recombination/dna Chain: B: PDB Molecule:recombinase flp protein; PDBTitle: flpe w330f mutant-dna holliday junction complex 23 c3lysC_ not modelled 68.9 3 PDB header:recombination Chain: C: PDB Molecule:prophage pi2 protein 01, integrase; PDBTitle: crystal structure of the n-terminal domain of the prophage2 pi2 protein 01 (integrase) from lactococcus lactis,3 northeast structural genomics consortium target kr124f 24 c2kj8A_ not modelled 65.9 5 PDB header:dna binding protein Chain: A: PDB Molecule:putative prophage cps-53 integrase; PDBTitle: nmr structure of fragment 87-196 from the putative phage2 integrase ints of e. coli: northeast structural genomics3 consortium target er652a, psi-2 25 c2kkvA_ not modelled 62.4 10 PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: solution nmr structure of an integrase domain from protein2 spa4288 from salmonella enterica, northeast structural3 genomics consortium target slr105h 26 c2kj9A_ not modelled 61.2 13 PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: nmr structure of intb phage-integrase-like protein fragment2 90-199 from erwinia carotova subsp. atroseptica: northeast3 structural genomics consortium target ewr217e 27 c2keyA_ not modelled 57.5 3 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative phage integrase; PDBTitle: solution nmr structure of a domain from a putative phage integrase2 protein bf2284 from bacteroides fragilis, northeast structural3 genomics consortium target bfr257c 28 c2khvA_ not modelled 49.0 10 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:phage integrase; PDBTitle: solution nmr structure of protein nmul_a0922 from2 nitrosospira multiformis. northeast structural genomics3 consortium target nmr38b. 29 d1p4ea2 not modelled 32.0 11 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 30 d1ofcx1 not modelled 21.2 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 31 c2b9sA_ not modelled 17.1 14 PDB header:isomerase/dna Chain: A: PDB Molecule:topoisomerase i-like protein; PDBTitle: crystal structure of heterodimeric l. donovani2 topoisomerase i-vanadate-dna complex 32 d1rr8c1 not modelled 16.8 16 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Eukaryotic DNA topoisomerase I, catalytic core 33 d1nvpb_ not modelled 15.3 26 Fold:Transcription factor IIA (TFIIA), alpha-helical domain Superfamily:Transcription factor IIA (TFIIA), alpha-helical domain Family:Transcription factor IIA (TFIIA), alpha-helical domain 34 c1nvpB_ not modelled 15.3 26 PDB header:transcription/dna Chain: B: PDB Molecule:transcription initiation factor iia alpha chain; PDBTitle: human tfiia/tbp/dna complex 35 d1a41a_ not modelled 11.2 13 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Eukaryotic DNA topoisomerase I, catalytic core 36 d1k4ta2 not modelled 11.2 16 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Eukaryotic DNA topoisomerase I, catalytic core 37 d1hvda_ not modelled 9.5 12 Fold:Annexin Superfamily:Annexin Family:Annexin 38 d1dwka1 not modelled 8.3 10 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Cyanase N-terminal domain 39 d1nh2b_ not modelled 7.5 19 Fold:Transcription factor IIA (TFIIA), alpha-helical domain Superfamily:Transcription factor IIA (TFIIA), alpha-helical domain Family:Transcription factor IIA (TFIIA), alpha-helical domain 40 d1fsea_ not modelled 6.9 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 41 d1bo9a_ not modelled 6.7 7 Fold:Annexin Superfamily:Annexin Family:Annexin 42 c1bo9A_ not modelled 6.7 7 PDB header:metal transport Chain: A: PDB Molecule:protein (annexin i); PDBTitle: nmr solution structure of domain 1 of human annexin i 43 d1i4aa_ not modelled 6.6 8 Fold:Annexin Superfamily:Annexin Family:Annexin 44 c3hh0C_ not modelled 6.6 13 PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus 45 d1m9ia2 not modelled 6.5 12 Fold:Annexin Superfamily:Annexin Family:Annexin 46 d1uoua1 not modelled 6.2 13 Fold:Methionine synthase domain-like Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 47 d1jhfa1 not modelled 6.1 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LexA repressor, N-terminal DNA-binding domain 48 d1m9ia1 not modelled 5.9 12 Fold:Annexin Superfamily:Annexin Family:Annexin 49 d2ie7a1 not modelled 5.3 14 Fold:Annexin Superfamily:Annexin Family:Annexin

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