Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	K	T	L	L	L	C	A	F	L	V	G	L	V	S	S	N	V	M	A	L	T	L	D	E	A	R	T	Q	G	R	V	G	E	T	F	Y	G	Y	L	V	A	L	K	T	D	A	E	T	E	K	L	V	A	D	I	N	A	E
Secondary structure
SS confidence
Disorder		?	?	?														?	?	?	?	?	?	?																						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.
Sequence		R	K	A	S	Y	Q	Q	L	A	K	Q	N	N	V	S	V	D	D	I	A	K	L	A	G	Q	K	L	V	A	R	A	K	P	G	E	Y	V	Q	G	I	N	G	K	W	V	R	K	F
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 1sg7 chain A domain 1 Region: 95 - 107 Aligned: 13 Modelled: 13 Confidence: 49.3% Identity: 46% Fold: ChaB-like Superfamily: ChaB-like Family: ChaB-like Phyre2 PDB 1sg7 chain A Region: 95 - 107 Aligned: 13 Modelled: 13 Confidence: 49.3% Identity: 46% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative cation transport regulator chab; PDBTitle: nmr solution structure of the putative cation transport2 regulator chab Phyre2 PDB 1lq1 chain A Region: 62 - 81 Aligned: 20 Modelled: 20 Confidence: 45.0% Identity: 25% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: Spo0A Phyre2 PDB 1fc3 chain A Region: 62 - 81 Aligned: 20 Modelled: 20 Confidence: 44.8% Identity: 25% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: Spo0A Phyre2 PDB 2ikb chain A domain 1 Region: 30 - 68 Aligned: 39 Modelled: 39 Confidence: 26.3% Identity: 31% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: NMB1012-like Phyre2 PDB 2l9y chain A Region: 65 - 103 Aligned: 39 Modelled: 39 Confidence: 22.3% Identity: 13% PDB header:sugar binding protein Chain: A: PDB Molecule:cvnh-lysm lectin; PDBTitle: solution structure of the mocvnh-lysm module from the rice blast2 fungus magnaporthe oryzae protein (mgg_03307) Phyre2 PDB 2nr7 chain A domain 1 Region: 30 - 72 Aligned: 43 Modelled: 43 Confidence: 21.7% Identity: 16% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: NMB1012-like Phyre2 PDB 2jna chain A domain 1 Region: 1 - 60 Aligned: 60 Modelled: 60 Confidence: 18.0% Identity: 15% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2k9i chain B Region: 66 - 90 Aligned: 25 Modelled: 25 Confidence: 17.3% 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 2cg4 chain B Region: 51 - 85 Aligned: 35 Modelled: 35 Confidence: 17.1% Identity: 23% PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc Phyre2 PDB 2bw2 chain A Region: 28 - 48 Aligned: 21 Modelled: 21 Confidence: 16.8% Identity: 14% PDB header:signaling protein Chain: A: PDB Molecule:bypass of forespore c; PDBTitle: bofc from bacillus subtilis Phyre2 PDB 1tty chain A Region: 65 - 82 Aligned: 18 Modelled: 18 Confidence: 14.6% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 1rk8 chain C Region: 98 - 106 Aligned: 9 Modelled: 9 Confidence: 14.4% Identity: 22% PDB header:translation Chain: C: PDB Molecule:within the bgcn gene intron protein; PDBTitle: structure of the cytosolic protein pym bound to the mago-2 y14 core of the exon junction complex Phyre2 PDB 1rk8 chain C Region: 98 - 106 Aligned: 9 Modelled: 9 Confidence: 14.4% Identity: 22% Fold: WW domain-like Superfamily: Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain Family: Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain Phyre2 PDB 3lpe chain F Region: 35 - 75 Aligned: 24 Modelled: 24 Confidence: 14.4% Identity: 25% PDB header:transferase Chain: F: PDB Molecule:dna-directed rna polymerase subunit e''; PDBTitle: crystal structure of spt4/5ngn heterodimer complex from methanococcus2 jannaschii Phyre2 PDB 1qqh chain A Region: 96 - 106 Aligned: 11 Modelled: 11 Confidence: 13.8% Identity: 27% Fold: E2 regulatory, transactivation domain Superfamily: E2 regulatory, transactivation domain Family: E2 regulatory, transactivation domain Phyre2 PDB 1mgt chain A Region: 65 - 102 Aligned: 38 Modelled: 38 Confidence: 13.6% Identity: 24% PDB header:transferase Chain: A: PDB Molecule:protein (o6-methylguanine-dna methyltransferase); PDBTitle: crystal structure of o6-methylguanine-dna methyltransferase from2 hyperthermophilic archaeon pyrococcus kodakaraensis strain kod1 Phyre2 PDB 1gzs chain B Region: 25 - 60 Aligned: 36 Modelled: 36 Confidence: 12.5% Identity: 17% Fold: SopE-like GEF domain Superfamily: SopE-like GEF domain Family: SopE-like GEF domain Phyre2 PDB 2cg4 chain A domain 1 Region: 51 - 82 Aligned: 32 Modelled: 32 Confidence: 12.5% Identity: 25% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Lrp/AsnC-like transcriptional regulator N-terminal domain Phyre2 PDB 2cyy chain A domain 1 Region: 51 - 82 Aligned: 32 Modelled: 32 Confidence: 11.8% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Lrp/AsnC-like transcriptional regulator N-terminal domain Phyre2 1 d1sg7a1 2 c1sg7A_ 3 d1lq1a_ 4 d1fc3a_ 5 d2ikba1 6 c2l9yA_ 7 d2nr7a1 8 d2jnaa1 9 c2k9iB_ 10 c2cg4B_ 11 c2bw2A_ 12 d1ttya_ 13 c1rk8C_ 14 d1rk8c_ 15 c3lpeF_ 16 d1qqha_ 17 c1mgtA_ 18 d1gzsb_ 19 d2cg4a1 20 d2cyya1 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

Detailed template information

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

1 d1sg7a1 49.3 46 Fold:ChaB-like Superfamily:ChaB-like Family:ChaB-like 2 c1sg7A_ 49.3 46 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative cation transport regulator chab; PDBTitle: nmr solution structure of the putative cation transport2 regulator chab 3 d1lq1a_ 45.0 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:Spo0A 4 d1fc3a_ 44.8 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:Spo0A 5 d2ikba1 26.3 31 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:NMB1012-like 6 c2l9yA_ 22.3 13 PDB header:sugar binding protein Chain: A: PDB Molecule:cvnh-lysm lectin; PDBTitle: solution structure of the mocvnh-lysm module from the rice blast2 fungus magnaporthe oryzae protein (mgg_03307) 7 d2nr7a1 21.7 16 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:NMB1012-like 8 d2jnaa1 18.0 15 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 9 c2k9iB_ 17.3 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 10 c2cg4B_ 17.1 23 PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc 11 c2bw2A_ 16.8 14 PDB header:signaling protein Chain: A: PDB Molecule:bypass of forespore c; PDBTitle: bofc from bacillus subtilis 12 d1ttya_ 14.6 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 13 c1rk8C_ 14.4 22 PDB header:translation Chain: C: PDB Molecule:within the bgcn gene intron protein; PDBTitle: structure of the cytosolic protein pym bound to the mago-2 y14 core of the exon junction complex 14 d1rk8c_ 14.4 22 Fold:WW domain-like Superfamily:Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain Family:Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain 15 c3lpeF_ 14.4 25 PDB header:transferase Chain: F: PDB Molecule:dna-directed rna polymerase subunit e''; PDBTitle: crystal structure of spt4/5ngn heterodimer complex from methanococcus2 jannaschii 16 d1qqha_ 13.8 27 Fold:E2 regulatory, transactivation domain Superfamily:E2 regulatory, transactivation domain Family:E2 regulatory, transactivation domain 17 c1mgtA_ 13.6 24 PDB header:transferase Chain: A: PDB Molecule:protein (o6-methylguanine-dna methyltransferase); PDBTitle: crystal structure of o6-methylguanine-dna methyltransferase from2 hyperthermophilic archaeon pyrococcus kodakaraensis strain kod1 18 d1gzsb_ 12.5 17 Fold:SopE-like GEF domain Superfamily:SopE-like GEF domain Family:SopE-like GEF domain 19 d2cg4a1 12.5 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 20 d2cyya1 11.8 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 21 c2ysaA_ not modelled 11.7 50 PDB header:metal binding protein Chain: A: PDB Molecule:retinoblastoma-binding protein 6; PDBTitle: solution structure of the zinc finger cchc domain from the2 human retinoblastoma-binding protein 6 (retinoblastoma-3 binding q protein 1, rbq-1) 22 d1tueb_ not modelled 11.6 27 Fold:E2 regulatory, transactivation domain Superfamily:E2 regulatory, transactivation domain Family:E2 regulatory, transactivation domain 23 c2o8xA_ not modelled 11.6 22 PDB header:transcription Chain: A: PDB Molecule:probable rna polymerase sigma-c factor; PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc 24 d1ku7a_ not modelled 11.3 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 25 d1r6ea_ not modelled 11.3 19 Fold:SopE-like GEF domain Superfamily:SopE-like GEF domain Family:SopE-like GEF domain 26 c1tueG_ not modelled 10.9 27 PDB header:replication Chain: G: PDB Molecule:regulatory protein e2; PDBTitle: the x-ray structure of the papillomavirus helicase in2 complex with its molecular matchmaker e2 27 c3frwF_ not modelled 10.5 16 PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum 28 d2ilaa_ not modelled 10.4 27 Fold:beta-Trefoil Superfamily:Cytokine Family:Interleukin-1 (IL-1) 29 c2c5kP_ not modelled 9.8 21 PDB header:protein transport Chain: P: PDB Molecule:vacuolar protein sorting protein 51; PDBTitle: n-terminal domain of tlg1 complexed with n-terminus of2 vps51 30 c1l0oC_ not modelled 9.6 12 PDB header:protein binding Chain: C: PDB Molecule:sigma factor; PDBTitle: crystal structure of the bacillus stearothermophilus anti-2 sigma factor spoiiab with the sporulation sigma factor3 sigmaf 31 d1l0oc_ not modelled 9.6 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 32 d1rp3a1 not modelled 9.6 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma3 domain 33 c3korD_ not modelled 9.4 16 PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus 34 c2dbbA_ not modelled 9.1 23 PDB header:transcriptional regulator Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061; PDBTitle: crystal structure of ph0061 35 c2fgtA_ not modelled 8.8 38 PDB header:signaling protein Chain: A: PDB Molecule:two-component system yycf/yycg regulatory PDBTitle: crystal structure of yych from bacillus subtilis 36 c2e1cA_ not modelled 8.6 14 PDB header:transcription/dna Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph1519; PDBTitle: structure of putative hth-type transcriptional regulator ph1519/dna2 complex 37 c3h8dC_ not modelled 8.4 21 PDB header:motor protein/signaling protein Chain: C: PDB Molecule:myosin-vi; PDBTitle: crystal structure of myosin vi in complex with dab2 peptide 38 d1qmha1 not modelled 8.4 13 Fold:Thioredoxin fold Superfamily:RNA 3'-terminal phosphate cyclase, RPTC, insert domain Family:RNA 3'-terminal phosphate cyclase, RPTC, insert domain 39 c2c5iP_ not modelled 8.2 21 PDB header:protein transport Chain: P: PDB Molecule:vacuolar protein sorting protein 51; PDBTitle: n-terminal domain of tlg1 complexed with n-terminus of2 vps51 in distorted conformation 40 c2bcmB_ not modelled 7.9 27 PDB header:cell adhesion Chain: B: PDB Molecule:f1845 fimbrial protein; PDBTitle: daae adhesin 41 d1e0ga_ not modelled 7.8 22 Fold:LysM domain Superfamily:LysM domain Family:LysM domain 42 d1z67a1 not modelled 7.7 18 Fold:YidB-like Superfamily:YidB-like Family:YidB-like 43 d1jhga_ not modelled 7.5 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 44 d1pn0a2 not modelled 7.5 17 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like 45 c1or7A_ not modelled 7.4 14 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma-e factor; PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea 46 c2ia0A_ not modelled 7.3 9 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative hth-type transcriptional regulator pf0864; PDBTitle: transcriptional regulatory protein pf0864 from pyrococcus furiosus a2 member of the asnc family (pf0864) 47 d1ut1a_ not modelled 7.1 27 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Dr-family adhesin 48 d1i1ga1 not modelled 7.1 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 49 d1h54a2 not modelled 7.1 25 Fold:Supersandwich Superfamily:Galactose mutarotase-like Family:Glycosyltransferase family 36 N-terminal domain 50 c1i1gA_ not modelled 7.0 11 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator lrpa; PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus 51 d2joka1 not modelled 6.8 40 Fold:SopE-like GEF domain Superfamily:SopE-like GEF domain Family:SopE-like GEF domain 52 c2djpA_ not modelled 6.8 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein sb145; PDBTitle: the solution structure of the lysm domain of human2 hypothetical protein sb145 53 d1mgta1 not modelled 6.6 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Methylated DNA-protein cysteine methyltransferase, C-terminal domain Family:Methylated DNA-protein cysteine methyltransferase, C-terminal domain 54 d1ofcx1 not modelled 6.5 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 55 d2a7wa1 not modelled 6.4 13 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:HisE-like (PRA-PH) 56 c2a7wF_ not modelled 6.4 13 PDB header:hydrolase Chain: F: PDB Molecule:phosphoribosyl-atp pyrophosphatase; PDBTitle: crystal structure of phosphoribosyl-atp pyrophosphatase2 from chromobacterium violaceum (atcc 12472). nesg target3 cvr7 57 c2opkC_ not modelled 6.1 27 PDB header:isomerase Chain: C: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a putative mannose-6-phosphate isomerase2 (reut_a1446) from ralstonia eutropha jmp134 at 2.10 a resolution 58 d1s6la1 not modelled 5.8 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MerB N-terminal domain-like 59 d2vera1 not modelled 5.8 20 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Dr-family adhesin 60 c2vbzA_ not modelled 5.5 23 PDB header:dna-binding protein Chain: A: PDB Molecule:transcriptional regulatory protein; PDBTitle: feast or famine regulatory protein (rv3291c)from m.2 tuberculosis complexed with l-tryptophan 61 c2krcA_ not modelled 5.4 12 PDB header:transcription Chain: A: PDB Molecule:dna-directed rna polymerase subunit delta; PDBTitle: solution structure of the n-terminal domain of bacillus2 subtilis delta subunit of rna polymerase 62 c2l4aA_ not modelled 5.4 11 PDB header:dna binding protein Chain: A: PDB Molecule:leucine responsive regulatory protein; PDBTitle: nmr structure of the dna-binding domain of e.coli lrp 63 d1or7a1 not modelled 5.1 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 64 d2cfxa1 not modelled 5.1 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-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