Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	Q	N	L	D	A	T	A	I	N	Q	I	H	A	L	I	S	A	Q	G	V	N	E	I	I	S	K	I	G	A	D	A	V	A	L	P	E	N	F	R	I	H	D	L	E	K	F	N	L	N	R	F	R	F	R	G	A	L	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?											?	?	?	?	?	?	?		?		?	?																	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	A	S	I	D	D	F	T	R	Y	S	K	D	L	A	D	E	G	T	R	C	F	I	D	A	D	N	M	R	A	V	S	V	L	N	L	G	T	I	D	E	P	G	H	A	D	N	T	A	T	L	K	L	K	K	T	A	P	F	S
Secondary structure
SS confidence
Disorder																																										?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	L	L	S	V	N	G	E	R	N	S	Q	K	S	L	A	E	W	I	E	D	W	A	D	Y	L	V	G	F	D	A	N	G	D	A	I	Q	A	T	K	A	A	A	A	I	R	K	I	T	I	E	A	N	Q	T	A	D	F	E	D
Secondary structure
SS confidence
Disorder						?	?	?	?	?	?	?																				?		?	?												?				?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		N	D	F	S	G	K	R	S	L	M	E	S	V	E	A	K	T	K	D	I	M	P	V	A	F	E	F	K	C	V	P	F	E	G	L	K	E	R	P	F	K	L	R	L	S	I	I	T	G	D	R	P	V	L	V	L	R	I	I	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.
Sequence		L	E	A	V	Q	E	D	M	A	N	E	F	R	D	L	L	V	E	K	F	K	D	S	K	V	E	T	F	I	G	T	F	T	A
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 1to0 chain A Region: 126 - 145 Aligned: 20 Modelled: 20 Confidence: 30.0% Identity: 30% Fold: alpha/beta knot Superfamily: alpha/beta knot Family: YbeA-like Phyre2 PDB 1ns5 chain A Region: 123 - 145 Aligned: 23 Modelled: 23 Confidence: 30.0% Identity: 26% Fold: alpha/beta knot Superfamily: alpha/beta knot Family: YbeA-like Phyre2 PDB 1vh0 chain A Region: 123 - 145 Aligned: 23 Modelled: 23 Confidence: 25.5% Identity: 22% Fold: alpha/beta knot Superfamily: alpha/beta knot Family: YbeA-like Phyre2 PDB 3cdd chain A domain 1 Region: 192 - 243 Aligned: 52 Modelled: 52 Confidence: 22.4% Identity: 15% Fold: Phage tail proteins Superfamily: Phage tail proteins Family: Baseplate protein-like Phyre2 PDB 1o6d chain A Region: 123 - 142 Aligned: 20 Modelled: 20 Confidence: 20.9% Identity: 25% Fold: alpha/beta knot Superfamily: alpha/beta knot Family: YbeA-like Phyre2 PDB 2gaa chain A Region: 33 - 75 Aligned: 42 Modelled: 43 Confidence: 16.1% Identity: 29% PDB header:unknown function Chain: A: PDB Molecule:hypothetical 39.9 kda protein; PDBTitle: crystal structure of yfh7 from saccharomyces cerevisiae: a2 putative p-loop containing kinase with a circular3 permutation. Phyre2 PDB 1cmr chain A Region: 103 - 108 Aligned: 6 Modelled: 6 Confidence: 15.4% Identity: 33% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Short-chain scorpion toxins Phyre2 PDB 1yku chain B Region: 133 - 199 Aligned: 67 Modelled: 67 Confidence: 13.5% Identity: 13% PDB header:unknown function Chain: B: PDB Molecule:hypothetical protein pxo2-61; PDBTitle: crystal structure of a sensor domain homolog Phyre2 PDB 3pq1 chain A Region: 241 - 272 Aligned: 31 Modelled: 32 Confidence: 12.0% Identity: 19% PDB header:transferase Chain: A: PDB Molecule:poly(a) rna polymerase; PDBTitle: crystal structure of human mitochondrial poly(a) polymerase (papd1) Phyre2 PDB 2al6 chain A domain 3 Region: 212 - 228 Aligned: 17 Modelled: 17 Confidence: 10.8% Identity: 18% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: First domain of FERM Phyre2 PDB 2gyc chain F domain 1 Region: 157 - 224 Aligned: 68 Modelled: 68 Confidence: 10.2% Identity: 12% Fold: Ribosomal protein L9 C-domain Superfamily: Ribosomal protein L9 C-domain Family: Ribosomal protein L9 C-domain Phyre2 PDB 1lli chain B Region: 114 - 170 Aligned: 57 Modelled: 57 Confidence: 9.5% Identity: 19% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 1x57 chain A domain 1 Region: 128 - 171 Aligned: 44 Modelled: 44 Confidence: 9.3% Identity: 16% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: EDF1-like Phyre2 PDB 3kts chain A Region: 35 - 86 Aligned: 51 Modelled: 52 Confidence: 8.7% Identity: 18% PDB header:transcriptional regulator Chain: A: PDB Molecule:glycerol uptake operon antiterminator regulatory protein; PDBTitle: crystal structure of glycerol uptake operon antiterminator regulatory2 protein from listeria monocytogenes str. 4b f2365 Phyre2 PDB 3q7c chain A Region: 121 - 210 Aligned: 77 Modelled: 90 Confidence: 8.7% Identity: 14% PDB header:hydrolase Chain: A: PDB Molecule:nucleoprotein; PDBTitle: exonuclease domain of lassa virus nucleoprotein bound to manganese Phyre2 PDB 1p71 chain A Region: 242 - 273 Aligned: 32 Modelled: 32 Confidence: 8.6% Identity: 13% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: Prokaryotic DNA-bending protein Phyre2 PDB 3bpj chain D Region: 135 - 167 Aligned: 33 Modelled: 33 Confidence: 8.2% Identity: 12% PDB header:translation Chain: D: PDB Molecule:eukaryotic translation initiation factor 3 subunit j; PDBTitle: crystal structure of human translation initiation factor 3, subunit 12 alpha Phyre2 PDB 1tii chain C Region: 62 - 73 Aligned: 12 Modelled: 12 Confidence: 8.0% Identity: 33% PDB header:enterotoxin Chain: C: PDB Molecule:heat labile enterotoxin type iib; PDBTitle: escherichia coli heat labile enterotoxin type iib Phyre2 PDB 3omt chain A Region: 128 - 170 Aligned: 43 Modelled: 43 Confidence: 7.6% Identity: 7% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae. Phyre2 PDB 2opk chain C Region: 102 - 112 Aligned: 11 Modelled: 11 Confidence: 7.6% Identity: 18% 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 Phyre2 1 d1to0a_ 2 d1ns5a_ 3 d1vh0a_ 4 d3cdda1 5 d1o6da_ 6 c2gaaA_ 7 d1cmra_ 8 c1ykuB_ 9 c3pq1A_ 10 d2al6a3 11 d2gycf1 12 d1llib_ 13 d1x57a1 14 c3ktsA_ 15 c3q7cA_ 16 d1p71a_ 17 c3bpjD_ 18 c1tiiC_ 19 c3omtA_ 20 c2opkC_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39

Detailed template information

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

1 d1to0a_ 30.0 30 Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like 2 d1ns5a_ 30.0 26 Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like 3 d1vh0a_ 25.5 22 Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like 4 d3cdda1 22.4 15 Fold:Phage tail proteins Superfamily:Phage tail proteins Family:Baseplate protein-like 5 d1o6da_ 20.9 25 Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like 6 c2gaaA_ 16.1 29 PDB header:unknown function Chain: A: PDB Molecule:hypothetical 39.9 kda protein; PDBTitle: crystal structure of yfh7 from saccharomyces cerevisiae: a2 putative p-loop containing kinase with a circular3 permutation. 7 d1cmra_ 15.4 33 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Short-chain scorpion toxins 8 c1ykuB_ 13.5 13 PDB header:unknown function Chain: B: PDB Molecule:hypothetical protein pxo2-61; PDBTitle: crystal structure of a sensor domain homolog 9 c3pq1A_ 12.0 19 PDB header:transferase Chain: A: PDB Molecule:poly(a) rna polymerase; PDBTitle: crystal structure of human mitochondrial poly(a) polymerase (papd1) 10 d2al6a3 10.8 18 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:First domain of FERM 11 d2gycf1 10.2 12 Fold:Ribosomal protein L9 C-domain Superfamily:Ribosomal protein L9 C-domain Family:Ribosomal protein L9 C-domain 12 d1llib_ 9.5 19 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 13 d1x57a1 9.3 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:EDF1-like 14 c3ktsA_ 8.7 18 PDB header:transcriptional regulator Chain: A: PDB Molecule:glycerol uptake operon antiterminator regulatory protein; PDBTitle: crystal structure of glycerol uptake operon antiterminator regulatory2 protein from listeria monocytogenes str. 4b f2365 15 c3q7cA_ 8.7 14 PDB header:hydrolase Chain: A: PDB Molecule:nucleoprotein; PDBTitle: exonuclease domain of lassa virus nucleoprotein bound to manganese 16 d1p71a_ 8.6 13 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 17 c3bpjD_ 8.2 12 PDB header:translation Chain: D: PDB Molecule:eukaryotic translation initiation factor 3 subunit j; PDBTitle: crystal structure of human translation initiation factor 3, subunit 12 alpha 18 c1tiiC_ 8.0 33 PDB header:enterotoxin Chain: C: PDB Molecule:heat labile enterotoxin type iib; PDBTitle: escherichia coli heat labile enterotoxin type iib 19 c3omtA_ 7.6 7 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae. 20 c2opkC_ 7.6 18 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 21 c3dnvB_ not modelled 7.4 18 PDB header:transcription/dna Chain: B: PDB Molecule:hth-type transcriptional regulator hipb; PDBTitle: mdt protein 22 c3bs3A_ not modelled 7.3 9 PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of a putative dna-binding protein from bacteroides2 fragilis 23 c3f6wE_ not modelled 7.2 14 PDB header:dna binding protein Chain: E: PDB Molecule:xre-family like protein; PDBTitle: xre-family like protein from pseudomonas syringae pv. tomato str.2 dc3000 24 c3nctC_ not modelled 6.7 18 PDB header:dna binding protein, chaperone Chain: C: PDB Molecule:protein psib; PDBTitle: x-ray crystal structure of the bacterial conjugation factor psib, a2 negative regulator of reca 25 d1vkfa_ not modelled 6.6 23 Fold:TIM beta/alpha-barrel Superfamily:GlpP-like Family:GlpP-like 26 c2np2B_ not modelled 6.4 22 PDB header:dna binding protein/dna Chain: B: PDB Molecule:hbb; PDBTitle: hbb-dna complex 27 c1r8jB_ not modelled 6.4 11 PDB header:circadian clock protein Chain: B: PDB Molecule:kaia; PDBTitle: crystal structure of circadian clock protein kaia from2 synechococcus elongatus 28 d1huua_ not modelled 6.3 13 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 29 c1qhhA_ not modelled 6.3 21 PDB header:hydrolase Chain: A: PDB Molecule:protein (pcra (subunit)); PDBTitle: structure of dna helicase with adpnp 30 d2a5yb2 not modelled 6.3 38 Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD 31 c3f52A_ not modelled 6.1 14 PDB header:transcription activator Chain: A: PDB Molecule:clp gene regulator (clgr); PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum 32 c2jvlA_ not modelled 6.1 10 PDB header:transcription Chain: A: PDB Molecule:trmbf1; PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei 33 c2ef8A_ not modelled 5.8 12 PDB header:transcription regulator Chain: A: PDB Molecule:putative transcription factor; PDBTitle: crystal structure of c.ecot38is 34 d1owfa_ not modelled 5.8 9 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 35 c3lisB_ not modelled 5.7 18 PDB header:transcription Chain: B: PDB Molecule:csp231i c protein; PDBTitle: crystal structure of the restriction-modification controller protein2 c.csp231i (monoclinic form) 36 d2auwa1 not modelled 5.6 14 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE0471 C-terminal domain-like 37 d2ppxa1 not modelled 5.6 8 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 38 c2ppxA_ not modelled 5.6 8 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atu1735; PDBTitle: crystal structure of a hth xre-family like protein from agrobacterium2 tumefaciens 39 c3nybA_ not modelled 5.5 9 PDB header:transferase/rna binding protein Chain: A: PDB Molecule:poly(a) rna polymerase protein 2; PDBTitle: structure and function of the polymerase core of tramp, a rna2 surveillance complex

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