Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	E	P	Q	R	L	F	F	A	I	D	L	P	A	E	I	R	E	Q	I	I	H	W	R	A	T	H	F	P	P	E	A	G	R	P	V	A	A	D	N	L	H	L	T	L	A	F	L	G	E	V	S	A	E	K	E	K	A	L
Secondary structure
SS confidence
Disorder		?	?	?	?																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	L	L	A	G	R	I	R	Q	P	G	F	T	L	T	L	D	D	A	G	Q	W	L	R	S	R	V	V	W	L	G	M	R	Q	P	P	R	G	L	I	Q	L	A	N	M	L	R	S	Q	A	A	R	S	G	C	F	Q	S	N	R
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.
Sequence		P	F	H	P	H	I	T	L	L	R	D	A	S	E	A	V	T	I	P	P	P	G	F	N	W	S	Y	A	V	T	E	F	T	L	Y	A	S	S	F	A	R	G	R	T	R	Y	T	P	L	K	R	W	A	L	T	Q
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 1iuh chain A Region: 5 - 175 Aligned: 169 Modelled: 170 Confidence: 100.0% Identity: 31% Fold: LigT-like Superfamily: LigT-like Family: 2'-5' RNA ligase LigT Phyre2 PDB 1vdx chain A Region: 5 - 176 Aligned: 170 Modelled: 172 Confidence: 100.0% Identity: 25% PDB header:ligase Chain: A: PDB Molecule:hypothetical protein ph0099; PDBTitle: crystal structure of a pyrococcus horikoshii protein with2 similarities to 2'5' rna-ligase Phyre2 PDB 2d4g chain A Region: 6 - 174 Aligned: 157 Modelled: 166 Confidence: 100.0% Identity: 18% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein bsu11850; PDBTitle: structure of yjcg protein, a putative 2'-5' rna ligase from2 bacillus subtilis Phyre2 PDB 2vfy chain A Region: 7 - 176 Aligned: 168 Modelled: 170 Confidence: 100.0% Identity: 13% PDB header:hydrolase Chain: A: PDB Molecule:akap18 delta; PDBTitle: akap18 delta central domain Phyre2 PDB 1jh6 chain A Region: 1 - 175 Aligned: 166 Modelled: 174 Confidence: 100.0% Identity: 14% Fold: LigT-like Superfamily: LigT-like Family: tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase Phyre2 PDB 2fsq chain A domain 1 Region: 11 - 139 Aligned: 125 Modelled: 129 Confidence: 98.2% Identity: 12% Fold: LigT-like Superfamily: LigT-like Family: Atu0111-like Phyre2 PDB 2ilx chain A domain 1 Region: 7 - 129 Aligned: 118 Modelled: 123 Confidence: 87.0% Identity: 18% Fold: LigT-like Superfamily: LigT-like Family: 2',3'-cyclic nucleotide 3'-phosphodiesterase, catalytic domain Phyre2 PDB 2e5c chain A Region: 1 - 82 Aligned: 78 Modelled: 82 Confidence: 38.6% Identity: 8% PDB header:transferase Chain: A: PDB Molecule:nicotinamide phosphoribosyltransferase; PDBTitle: crystal structure of human nmprtase complexed with 5'-phosphoribosyl-2 1'-pyrophosphate Phyre2 PDB 2i3e chain A Region: 7 - 100 Aligned: 92 Modelled: 94 Confidence: 28.4% Identity: 18% PDB header:hydrolase Chain: A: PDB Molecule:g-rich; PDBTitle: solution structure of catalytic domain of goldfish rich2 protein Phyre2 PDB 3h0d chain B Region: 147 - 176 Aligned: 28 Modelled: 30 Confidence: 18.8% Identity: 11% PDB header:transcription/dna Chain: B: PDB Molecule:ctsr; PDBTitle: crystal structure of ctsr in complex with a 26bp dna duplex Phyre2 PDB 3ce8 chain A Region: 44 - 117 Aligned: 71 Modelled: 74 Confidence: 18.6% Identity: 17% PDB header:unknown function Chain: A: PDB Molecule:putative pii-like nitrogen regulatory protein; PDBTitle: crystal structure of a duf3240 family protein (sbal_0098) from2 shewanella baltica os155 at 2.40 a resolution Phyre2 PDB 1gyx chain A Region: 42 - 67 Aligned: 26 Modelled: 26 Confidence: 14.4% Identity: 19% Fold: Tautomerase/MIF Superfamily: Tautomerase/MIF Family: 4-oxalocrotonate tautomerase-like Phyre2 PDB 2qpq chain C Region: 46 - 118 Aligned: 69 Modelled: 73 Confidence: 11.0% Identity: 13% PDB header:transport protein Chain: C: PDB Molecule:protein bug27; PDBTitle: structure of bug27 from bordetella pertussis Phyre2 PDB 3itf chain A Region: 2 - 66 Aligned: 65 Modelled: 62 Confidence: 9.2% Identity: 14% PDB header:signaling protein Chain: A: PDB Molecule:periplasmic adaptor protein cpxp; PDBTitle: structural basis for the inhibitory function of the cpxp adaptor2 protein Phyre2 PDB 3noh chain A Region: 81 - 124 Aligned: 44 Modelled: 44 Confidence: 9.2% Identity: 11% PDB header:peptide binding protein Chain: A: PDB Molecule:putative peptide binding protein; PDBTitle: crystal structure of a putative peptide binding protein (rumgna_00914)2 from ruminococcus gnavus atcc 29149 at 1.60 a resolution Phyre2 PDB 1aop chain A domain 2 Region: 6 - 71 Aligned: 59 Modelled: 66 Confidence: 8.9% Identity: 15% Fold: Ferredoxin-like Superfamily: Nitrite/Sulfite reductase N-terminal domain-like Family: Duplicated SiR/NiR-like domains 1 and 3 Phyre2 PDB 1u8s chain A domain 1 Region: 43 - 125 Aligned: 80 Modelled: 80 Confidence: 8.5% Identity: 11% Fold: Ferredoxin-like Superfamily: ACT-like Family: Glycine cleavage system transcriptional repressor Phyre2 PDB 1zj8 chain B Region: 6 - 127 Aligned: 114 Modelled: 122 Confidence: 7.8% Identity: 10% PDB header:oxidoreductase Chain: B: PDB Molecule:probable ferredoxin-dependent nitrite reductase nira; PDBTitle: structure of mycobacterium tuberculosis nira protein Phyre2 PDB 2ih2 chain A domain 2 Region: 123 - 156 Aligned: 33 Modelled: 34 Confidence: 7.8% Identity: 18% Fold: DNA methylase specificity domain Superfamily: DNA methylase specificity domain Family: TaqI C-terminal domain-like Phyre2 PDB 3dku chain B Region: 122 - 129 Aligned: 8 Modelled: 8 Confidence: 7.8% Identity: 50% PDB header:hydrolase Chain: B: PDB Molecule:putative phosphohydrolase; PDBTitle: crystal structure of nudix hydrolase orf153, ymfb, from2 escherichia coli k-1 Phyre2 1 d1iuha_ 2 c1vdxA_ 3 c2d4gA_ 4 c2vfyA_ 5 d1jh6a_ 6 d2fsqa1 7 d2ilxa1 8 c2e5cA_ 9 c2i3eA_ 10 c3h0dB_ 11 c3ce8A_ 12 d1gyxa_ 13 c2qpqC_ 14 c3itfA_ 15 c3nohA_ 16 d1aopa2 17 d1u8sa1 18 c1zj8B_ 19 d2ih2a2 20 c3dkuB_ 21

Detailed template information

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

1 d1iuha_ 100.0 31 Fold:LigT-like Superfamily:LigT-like Family:2'-5' RNA ligase LigT 2 c1vdxA_ 100.0 25 PDB header:ligase Chain: A: PDB Molecule:hypothetical protein ph0099; PDBTitle: crystal structure of a pyrococcus horikoshii protein with2 similarities to 2'5' rna-ligase 3 c2d4gA_ 100.0 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein bsu11850; PDBTitle: structure of yjcg protein, a putative 2'-5' rna ligase from2 bacillus subtilis 4 c2vfyA_ 100.0 13 PDB header:hydrolase Chain: A: PDB Molecule:akap18 delta; PDBTitle: akap18 delta central domain 5 d1jh6a_ 100.0 14 Fold:LigT-like Superfamily:LigT-like Family:tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase 6 d2fsqa1 98.2 12 Fold:LigT-like Superfamily:LigT-like Family:Atu0111-like 7 d2ilxa1 87.0 18 Fold:LigT-like Superfamily:LigT-like Family:2',3'-cyclic nucleotide 3'-phosphodiesterase, catalytic domain 8 c2e5cA_ 38.6 8 PDB header:transferase Chain: A: PDB Molecule:nicotinamide phosphoribosyltransferase; PDBTitle: crystal structure of human nmprtase complexed with 5'-phosphoribosyl-2 1'-pyrophosphate 9 c2i3eA_ 28.4 18 PDB header:hydrolase Chain: A: PDB Molecule:g-rich; PDBTitle: solution structure of catalytic domain of goldfish rich2 protein 10 c3h0dB_ 18.8 11 PDB header:transcription/dna Chain: B: PDB Molecule:ctsr; PDBTitle: crystal structure of ctsr in complex with a 26bp dna duplex 11 c3ce8A_ 18.6 17 PDB header:unknown function Chain: A: PDB Molecule:putative pii-like nitrogen regulatory protein; PDBTitle: crystal structure of a duf3240 family protein (sbal_0098) from2 shewanella baltica os155 at 2.40 a resolution 12 d1gyxa_ 14.4 19 Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:4-oxalocrotonate tautomerase-like 13 c2qpqC_ 11.0 13 PDB header:transport protein Chain: C: PDB Molecule:protein bug27; PDBTitle: structure of bug27 from bordetella pertussis 14 c3itfA_ 9.2 14 PDB header:signaling protein Chain: A: PDB Molecule:periplasmic adaptor protein cpxp; PDBTitle: structural basis for the inhibitory function of the cpxp adaptor2 protein 15 c3nohA_ 9.2 11 PDB header:peptide binding protein Chain: A: PDB Molecule:putative peptide binding protein; PDBTitle: crystal structure of a putative peptide binding protein (rumgna_00914)2 from ruminococcus gnavus atcc 29149 at 1.60 a resolution 16 d1aopa2 8.9 15 Fold:Ferredoxin-like Superfamily:Nitrite/Sulfite reductase N-terminal domain-like Family:Duplicated SiR/NiR-like domains 1 and 3 17 d1u8sa1 8.5 11 Fold:Ferredoxin-like Superfamily:ACT-like Family:Glycine cleavage system transcriptional repressor 18 c1zj8B_ 7.8 10 PDB header:oxidoreductase Chain: B: PDB Molecule:probable ferredoxin-dependent nitrite reductase nira; PDBTitle: structure of mycobacterium tuberculosis nira protein 19 d2ih2a2 7.8 18 Fold:DNA methylase specificity domain Superfamily:DNA methylase specificity domain Family:TaqI C-terminal domain-like 20 c3dkuB_ 7.8 50 PDB header:hydrolase Chain: B: PDB Molecule:putative phosphohydrolase; PDBTitle: crystal structure of nudix hydrolase orf153, ymfb, from2 escherichia coli k-1 21 d1owfb_ not modelled 6.0 10 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein

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