Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	E	T	K	N	E	L	E	D	L	L	E	K	A	A	T	E	P	A	H	R	P	A	F	F	R	T	L	L	E	S	T	V	W	V	P	G	T	A	A	Q	G	E	A	V	V	E	D	S	A	L	D	L	Q	H	W	E	K	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?										?	?	?	?	?	?																			?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	G	T	S	V	I	P	F	F	T	S	L	E	A	L	Q	Q	A	V	E	D	E	Q	A	F	V	V	M	P	V	R	T	L	F	E	M	T	L	G	E	T	L	F	L	N	A	K	L	P	T	G	K	E	F	M	P	R	E	I	S
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	L	I	G	E	E	G	N	P	L	S	S	Q	E	I	L	E	G	G	E	S	L	I	L	S	E	V	A	E	P	P	A	Q	M	I	D	S	L	T	T	L	F	K	T	I	K	P	V	K	R	A	F	I	C	S	I	K	E	N	E
Secondary structure
SS confidence
Disorder					?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?		?	?		?		?	?	?	?														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		E	A	Q	P	N	L	L	I	G	I	E	A	D	G	D	I	E	E	I	I	Q	A	T	G	S	V	A	T	D	T	L	P	G	D	E	P	I	D	I	C	Q	V	K	K	G	E	K	G	I	S	H	F	I	T	E	H	I	A	P	F
Secondary structure
SS confidence
Disorder																																?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.
Sequence		Y	E	R	R	W	G	G	F	L	R	D	F	K	Q	N	R	I	I
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 1no5 chain A Region: 149 - 244 Aligned: 94 Modelled: 96 Confidence: 40.2% Identity: 13% Fold: Nucleotidyltransferase Superfamily: Nucleotidyltransferase Family: Catalytic subunit of bi-partite nucleotidyltransferase Phyre2 PDB 1r7g chain A Region: 246 - 252 Aligned: 7 Modelled: 7 Confidence: 29.2% Identity: 57% PDB header:membrane protein Chain: A: PDB Molecule:genome polyprotein; PDBTitle: nmr structure of the membrane anchor domain (1-31) of the2 nonstructural protein 5a (ns5a) of hepatitis c virus3 (minimized average structure, sample in 100mm dpc) Phyre2 PDB 2l8t chain A Region: 242 - 258 Aligned: 17 Modelled: 17 Confidence: 20.9% Identity: 47% PDB header:structural protein Chain: A: PDB Molecule:transposon tn557 toxic shock syndrome toxin-1; PDBTitle: staphylococcus aureus pathogenicity island 1 protein gp6, an internal2 scaffold in size determination Phyre2 PDB 2aby chain A Region: 2 - 18 Aligned: 17 Modelled: 17 Confidence: 12.4% Identity: 29% PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein ta0743; PDBTitle: solution structure of ta0743 from thermoplasma acidophilum Phyre2 PDB 2rff chain A Region: 154 - 249 Aligned: 90 Modelled: 96 Confidence: 12.1% Identity: 13% PDB header:transferase Chain: A: PDB Molecule:putative nucleotidyltransferase; PDBTitle: crystal structure of a putative nucleotidyltransferase2 (np_343093.1) from sulfolobus solfataricus at 1.40 a3 resolution Phyre2 PDB 1wot chain A Region: 152 - 240 Aligned: 85 Modelled: 89 Confidence: 11.8% Identity: 14% Fold: Nucleotidyltransferase Superfamily: Nucleotidyltransferase Family: Catalytic subunit of bi-partite nucleotidyltransferase Phyre2 PDB 2fok chain A domain 2 Region: 241 - 252 Aligned: 12 Modelled: 12 Confidence: 9.0% Identity: 42% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Restriction endonuclease FokI, N-terminal (recognition) domain Phyre2 PDB 1dd5 chain A Region: 88 - 172 Aligned: 78 Modelled: 85 Confidence: 8.6% Identity: 14% Fold: RRF/tRNA synthetase additional domain-like Superfamily: Ribosome recycling factor, RRF Family: Ribosome recycling factor, RRF Phyre2 PDB 3r1f chain O Region: 106 - 174 Aligned: 61 Modelled: 69 Confidence: 8.0% Identity: 18% PDB header:transcription Chain: O: PDB Molecule:esx-1 secretion-associated regulator espr; PDBTitle: crystal structure of a key regulator of virulence in mycobacterium2 tuberculosis Phyre2 PDB 1ge9 chain A Region: 88 - 172 Aligned: 77 Modelled: 85 Confidence: 7.4% Identity: 12% Fold: RRF/tRNA synthetase additional domain-like Superfamily: Ribosome recycling factor, RRF Family: Ribosome recycling factor, RRF Phyre2 PDB 1ek8 chain A Region: 88 - 172 Aligned: 78 Modelled: 85 Confidence: 7.3% Identity: 15% Fold: RRF/tRNA synthetase additional domain-like Superfamily: Ribosome recycling factor, RRF Family: Ribosome recycling factor, RRF Phyre2 PDB 1a3a chain A Region: 140 - 187 Aligned: 48 Modelled: 48 Confidence: 6.9% Identity: 17% Fold: Phoshotransferase/anion transport protein Superfamily: Phoshotransferase/anion transport protein Family: IIA domain of mannitol-specific and ntr phosphotransferase EII Phyre2 PDB 1s6l chain A domain 2 Region: 65 - 96 Aligned: 32 Modelled: 32 Confidence: 6.2% Identity: 19% Fold: NosL/MerB-like Superfamily: NosL/MerB-like Family: MerB-like Phyre2 PDB 3cu2 chain A Region: 64 - 109 Aligned: 46 Modelled: 46 Confidence: 6.1% Identity: 15% PDB header:isomerase Chain: A: PDB Molecule:ribulose-5-phosphate 3-epimerase; PDBTitle: crystal structure of ribulose-5-phosphate 3-epimerase (yp_718263.1)2 from haemophilus somnus 129pt at 1.91 a resolution Phyre2 PDB 1eh1 chain A Region: 88 - 172 Aligned: 78 Modelled: 85 Confidence: 5.9% Identity: 9% Fold: RRF/tRNA synthetase additional domain-like Superfamily: Ribosome recycling factor, RRF Family: Ribosome recycling factor, RRF Phyre2 PDB 1sm4 chain A domain 2 Region: 105 - 180 Aligned: 71 Modelled: 76 Confidence: 5.8% Identity: 10% Fold: Ferredoxin reductase-like, C-terminal NADP-linked domain Superfamily: Ferredoxin reductase-like, C-terminal NADP-linked domain Family: Reductases Phyre2 PDB 1is1 chain A Region: 88 - 172 Aligned: 78 Modelled: 85 Confidence: 5.8% Identity: 10% Fold: RRF/tRNA synthetase additional domain-like Superfamily: Ribosome recycling factor, RRF Family: Ribosome recycling factor, RRF Phyre2 PDB 2qmw chain A domain 2 Region: 141 - 210 Aligned: 67 Modelled: 69 Confidence: 5.5% Identity: 12% Fold: Ferredoxin-like Superfamily: ACT-like Family: Phenylalanine metabolism regulatory domain Phyre2 PDB 3gny chain A Region: 240 - 248 Aligned: 9 Modelled: 9 Confidence: 5.4% Identity: 33% PDB header:antimicrobial protein Chain: A: PDB Molecule:neutrophil defensin 1; PDBTitle: crystal structure of human alpha-defensin 1 (hnp1) Phyre2 PDB 3hj2 chain B Region: 240 - 248 Aligned: 9 Modelled: 9 Confidence: 5.2% Identity: 33% PDB header:antimicrobial protein Chain: B: PDB Molecule:human neutrophil peptide 1; PDBTitle: crystal structure of covalent dimer of hnp1 Phyre2 1 d1no5a_ 2 c1r7gA_ 3 c2l8tA_ 4 c2abyA_ 5 c2rffA_ 6 d1wota_ 7 d2foka2 8 d1dd5a_ 9 c3r1fO_ 10 d1ge9a_ 11 d1ek8a_ 12 d1a3aa_ 13 d1s6la2 14 c3cu2A_ 15 d1eh1a_ 16 d1sm4a2 17 d1is1a_ 18 d2qmwa2 19 c3gnyA_ 20 c3hj2B_ 21

Detailed template information

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

1 d1no5a_ 40.2 13 Fold:Nucleotidyltransferase Superfamily:Nucleotidyltransferase Family:Catalytic subunit of bi-partite nucleotidyltransferase 2 c1r7gA_ 29.2 57 PDB header:membrane protein Chain: A: PDB Molecule:genome polyprotein; PDBTitle: nmr structure of the membrane anchor domain (1-31) of the2 nonstructural protein 5a (ns5a) of hepatitis c virus3 (minimized average structure, sample in 100mm dpc) 3 c2l8tA_ 20.9 47 PDB header:structural protein Chain: A: PDB Molecule:transposon tn557 toxic shock syndrome toxin-1; PDBTitle: staphylococcus aureus pathogenicity island 1 protein gp6, an internal2 scaffold in size determination 4 c2abyA_ 12.4 29 PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein ta0743; PDBTitle: solution structure of ta0743 from thermoplasma acidophilum 5 c2rffA_ 12.1 13 PDB header:transferase Chain: A: PDB Molecule:putative nucleotidyltransferase; PDBTitle: crystal structure of a putative nucleotidyltransferase2 (np_343093.1) from sulfolobus solfataricus at 1.40 a3 resolution 6 d1wota_ 11.8 14 Fold:Nucleotidyltransferase Superfamily:Nucleotidyltransferase Family:Catalytic subunit of bi-partite nucleotidyltransferase 7 d2foka2 9.0 42 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Restriction endonuclease FokI, N-terminal (recognition) domain 8 d1dd5a_ 8.6 14 Fold:RRF/tRNA synthetase additional domain-like Superfamily:Ribosome recycling factor, RRF Family:Ribosome recycling factor, RRF 9 c3r1fO_ 8.0 18 PDB header:transcription Chain: O: PDB Molecule:esx-1 secretion-associated regulator espr; PDBTitle: crystal structure of a key regulator of virulence in mycobacterium2 tuberculosis 10 d1ge9a_ 7.4 12 Fold:RRF/tRNA synthetase additional domain-like Superfamily:Ribosome recycling factor, RRF Family:Ribosome recycling factor, RRF 11 d1ek8a_ 7.3 15 Fold:RRF/tRNA synthetase additional domain-like Superfamily:Ribosome recycling factor, RRF Family:Ribosome recycling factor, RRF 12 d1a3aa_ 6.9 17 Fold:Phoshotransferase/anion transport protein Superfamily:Phoshotransferase/anion transport protein Family:IIA domain of mannitol-specific and ntr phosphotransferase EII 13 d1s6la2 6.2 19 Fold:NosL/MerB-like Superfamily:NosL/MerB-like Family:MerB-like 14 c3cu2A_ 6.1 15 PDB header:isomerase Chain: A: PDB Molecule:ribulose-5-phosphate 3-epimerase; PDBTitle: crystal structure of ribulose-5-phosphate 3-epimerase (yp_718263.1)2 from haemophilus somnus 129pt at 1.91 a resolution 15 d1eh1a_ 5.9 9 Fold:RRF/tRNA synthetase additional domain-like Superfamily:Ribosome recycling factor, RRF Family:Ribosome recycling factor, RRF 16 d1sm4a2 5.8 10 Fold:Ferredoxin reductase-like, C-terminal NADP-linked domain Superfamily:Ferredoxin reductase-like, C-terminal NADP-linked domain Family:Reductases 17 d1is1a_ 5.8 10 Fold:RRF/tRNA synthetase additional domain-like Superfamily:Ribosome recycling factor, RRF Family:Ribosome recycling factor, RRF 18 d2qmwa2 5.5 12 Fold:Ferredoxin-like Superfamily:ACT-like Family:Phenylalanine metabolism regulatory domain 19 c3gnyA_ 5.4 33 PDB header:antimicrobial protein Chain: A: PDB Molecule:neutrophil defensin 1; PDBTitle: crystal structure of human alpha-defensin 1 (hnp1) 20 c3hj2B_ 5.2 33 PDB header:antimicrobial protein Chain: B: PDB Molecule:human neutrophil peptide 1; PDBTitle: crystal structure of covalent dimer of hnp1 21 c3ns5B_ not modelled 5.1 17 PDB header:translation Chain: B: PDB Molecule:eukaryotic translation initiation factor 3 subunit b; PDBTitle: crystal structure of the rna recognition motif of yeast eif3b residues2 76-161

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