Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	K	Q	V	E	I	F	T	D	G	S	C	L	G	N	P	G	P	G	G	Y	G	A	I	L	R	Y	R	G	R	E	K	T	F	S	A	G	Y	T	R	T	T	N	N	R	M	E	L	M	A	A	I	V	A	L	E	A	L	K
Secondary structure
SS confidence
Disorder		?	?	?													?																						?			?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		E	H	C	E	V	I	L	S	T	D	S	Q	Y	V	R	Q	G	I	T	Q	W	I	H	N	W	K	K	R	G	W	K	T	A	D	K	K	P	V	K	N	V	D	L	W	Q	R	L	D	A	A	L	G	Q	H	Q	I	K	W	E	W
Secondary structure
SS confidence
Disorder																												?	?		?	?	?	?	?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.
Sequence		V	K	G	H	A	G	H	P	E	N	E	R	C	D	E	L	A	R	A	A	A	M	N	P	T	L	E	D	T	G	Y	Q	V	E	V
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 1jl1 chain A Region: 3 - 154 Aligned: 152 Modelled: 152 Confidence: 100.0% Identity: 97% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Ribonuclease H Phyre2 PDB 1jl2 chain A Region: 3 - 151 Aligned: 149 Modelled: 149 Confidence: 100.0% Identity: 74% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Ribonuclease H Phyre2 PDB 2e4l chain A Region: 2 - 154 Aligned: 153 Modelled: 153 Confidence: 100.0% Identity: 70% PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease hi; PDBTitle: thermodynamic and structural analysis of thermolabile rnase hi from2 shewanella oneidensis mr-1 Phyre2 PDB 1wsi chain B Region: 2 - 153 Aligned: 149 Modelled: 152 Confidence: 100.0% Identity: 99% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Ribonuclease H Phyre2 PDB 1ril chain A Region: 2 - 145 Aligned: 144 Modelled: 144 Confidence: 100.0% Identity: 56% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Ribonuclease H Phyre2 PDB 3h08 chain B Region: 3 - 142 Aligned: 139 Modelled: 140 Confidence: 100.0% Identity: 45% PDB header:hydrolase Chain: B: PDB Molecule:rnh (ribonuclease h); PDBTitle: crystal structure of the ribonuclease h1 from chlorobium2 tepidum Phyre2 PDB 2qkk chain I Region: 1 - 144 Aligned: 144 Modelled: 144 Confidence: 100.0% Identity: 35% PDB header:hydrolase/dna/rna Chain: I: PDB Molecule:ribonuclease h1; PDBTitle: human rnase h catalytic domain mutant d210n in complex with2 14-mer rna/dna hybrid Phyre2 PDB 2hb5 chain A Region: 3 - 149 Aligned: 134 Modelled: 147 Confidence: 100.0% Identity: 28% PDB header:hydrolase Chain: A: PDB Molecule:reverse transcriptase/ribonuclease h; PDBTitle: crystal structure of the moloney murine leukemia virus2 rnase h domain Phyre2 PDB 1eet chain A domain 1 Region: 5 - 142 Aligned: 120 Modelled: 125 Confidence: 99.9% Identity: 27% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Ribonuclease H Phyre2 PDB 1mu2 chain A domain 1 Region: 4 - 140 Aligned: 119 Modelled: 124 Confidence: 99.9% Identity: 26% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Ribonuclease H Phyre2 PDB 1jla chain A domain 1 Region: 1 - 137 Aligned: 119 Modelled: 124 Confidence: 99.9% Identity: 26% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Ribonuclease H Phyre2 PDB 1zbf chain A domain 1 Region: 7 - 134 Aligned: 124 Modelled: 128 Confidence: 99.9% Identity: 21% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Ribonuclease H Phyre2 PDB 2kq2 chain A Region: 4 - 147 Aligned: 129 Modelled: 129 Confidence: 99.9% Identity: 22% PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease h-related protein; PDBTitle: solution nmr structure of the apo form of a ribonuclease h2 domain of protein dsy1790 from desulfitobacterium3 hafniense, northeast structural genomics target dhr1a Phyre2 PDB 2rpi chain A Region: 3 - 122 Aligned: 99 Modelled: 99 Confidence: 99.9% Identity: 63% PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease h; PDBTitle: the nmr structure of the submillisecond folding2 intermediate of the thermus thermophilus ribonuclease h Phyre2 PDB 1o1w chain A Region: 1 - 143 Aligned: 125 Modelled: 130 Confidence: 99.9% Identity: 26% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Ribonuclease H Phyre2 PDB 3hst chain D Region: 4 - 142 Aligned: 125 Modelled: 139 Confidence: 99.9% Identity: 31% PDB header:hydrolase Chain: D: PDB Molecule:protein rv2228c/mt2287; PDBTitle: n-terminal rnase h domain of rv2228c from mycobacterium tuberculosis2 as a fusion protein with maltose binding protein Phyre2 PDB 1mu2 chain A Region: 5 - 140 Aligned: 118 Modelled: 121 Confidence: 99.9% Identity: 25% PDB header:transferase Chain: A: PDB Molecule:hiv-2 rt; PDBTitle: crystal structure of hiv-2 reverse transcriptase Phyre2 PDB 2ehg chain A Region: 5 - 142 Aligned: 123 Modelled: 126 Confidence: 99.8% Identity: 24% PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease hi; PDBTitle: crystal structure of hyperthermophilic archaeal rnase hi Phyre2 PDB 1s9g chain A domain 1 Region: 5 - 127 Aligned: 105 Modelled: 110 Confidence: 99.8% Identity: 26% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Ribonuclease H Phyre2 PDB 1s1t chain A domain 1 Region: 5 - 124 Aligned: 102 Modelled: 107 Confidence: 99.8% Identity: 25% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Ribonuclease H Phyre2 1 d1jl1a_ 2 d1jl2a_ 3 c2e4lA_ 4 d1wsib_ 5 d1rila_ 6 c3h08B_ 7 c2qkkI_ 8 c2hb5A_ 9 d1eeta1 10 d1mu2a1 11 d1jlaa1 12 d1zbfa1 13 c2kq2A_ 14 c2rpiA_ 15 d1o1wa_ 16 c3hstD_ 17 c1mu2A_ 18 c2ehgA_ 19 d1s9ga1 20 d1s1ta1 21 22 23 24 25 26 27 28 29 30 31 32 33 34

Detailed template information

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

1 d1jl1a_ 100.0 97 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H 2 d1jl2a_ 100.0 74 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H 3 c2e4lA_ 100.0 70 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease hi; PDBTitle: thermodynamic and structural analysis of thermolabile rnase hi from2 shewanella oneidensis mr-1 4 d1wsib_ 100.0 99 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H 5 d1rila_ 100.0 56 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H 6 c3h08B_ 100.0 45 PDB header:hydrolase Chain: B: PDB Molecule:rnh (ribonuclease h); PDBTitle: crystal structure of the ribonuclease h1 from chlorobium2 tepidum 7 c2qkkI_ 100.0 35 PDB header:hydrolase/dna/rna Chain: I: PDB Molecule:ribonuclease h1; PDBTitle: human rnase h catalytic domain mutant d210n in complex with2 14-mer rna/dna hybrid 8 c2hb5A_ 100.0 28 PDB header:hydrolase Chain: A: PDB Molecule:reverse transcriptase/ribonuclease h; PDBTitle: crystal structure of the moloney murine leukemia virus2 rnase h domain 9 d1eeta1 99.9 27 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H 10 d1mu2a1 99.9 26 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H 11 d1jlaa1 99.9 26 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H 12 d1zbfa1 99.9 21 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H 13 c2kq2A_ 99.9 22 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease h-related protein; PDBTitle: solution nmr structure of the apo form of a ribonuclease h2 domain of protein dsy1790 from desulfitobacterium3 hafniense, northeast structural genomics target dhr1a 14 c2rpiA_ 99.9 63 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease h; PDBTitle: the nmr structure of the submillisecond folding2 intermediate of the thermus thermophilus ribonuclease h 15 d1o1wa_ 99.9 26 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H 16 c3hstD_ 99.9 31 PDB header:hydrolase Chain: D: PDB Molecule:protein rv2228c/mt2287; PDBTitle: n-terminal rnase h domain of rv2228c from mycobacterium tuberculosis2 as a fusion protein with maltose binding protein 17 c1mu2A_ 99.9 25 PDB header:transferase Chain: A: PDB Molecule:hiv-2 rt; PDBTitle: crystal structure of hiv-2 reverse transcriptase 18 c2ehgA_ 99.8 24 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease hi; PDBTitle: crystal structure of hyperthermophilic archaeal rnase hi 19 d1s9ga1 99.8 26 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H 20 d1s1ta1 99.8 25 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H 21 c1rthA_ not modelled 99.6 26 PDB header:nucleotidyltransferase Chain: A: PDB Molecule:hiv-1 reverse transcriptase; PDBTitle: high resolution structures of hiv-1 rt from four rt-2 inhibitor complexes 22 c2opqA_ not modelled 99.2 27 PDB header:transferase Chain: A: PDB Molecule:reverse transcriptase/ribonuclease h; PDBTitle: crystal structure of l100i mutant hiv-1 reverse2 transcriptase in complex with gw420867x. 23 d1rw3a_ not modelled 56.1 8 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Reverse transcriptase 24 c2hxvA_ not modelled 22.7 17 PDB header:biosynthetic protein Chain: A: PDB Molecule:diaminohydroxyphosphoribosylaminopyrimidine deaminase/ 5- PDBTitle: crystal structure of a diaminohydroxyphosphoribosylaminopyrimidine2 deaminase/ 5-amino-6-(5-phosphoribosylamino)uracil reductase (tm1828)3 from thermotoga maritima at 1.80 a resolution 25 d2b3za2 not modelled 13.1 16 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Deoxycytidylate deaminase-like 26 c3hl4B_ not modelled 11.5 23 PDB header:transferase Chain: B: PDB Molecule:choline-phosphate cytidylyltransferase a; PDBTitle: crystal structure of a mammalian ctp:phosphocholine2 cytidylyltransferase with cdp-choline 27 d1ynja1 not modelled 9.4 63 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RNA polymerase alpha subunit dimerisation domain 28 d1nuia2 not modelled 9.4 38 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:DNA primase zinc finger 29 d2g84a1 not modelled 9.2 19 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Deoxycytidylate deaminase-like 30 d1mr4a_ not modelled 8.2 63 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Plant defensins 31 d1cw0a_ not modelled 8.1 36 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Very short patch repair (VSR) endonuclease 32 d1vsra_ not modelled 7.8 36 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Very short patch repair (VSR) endonuclease 33 c2d5nB_ not modelled 7.3 22 PDB header:hydrolase, oxidoreductase Chain: B: PDB Molecule:riboflavin biosynthesis protein ribd; PDBTitle: crystal structure of a bifunctional deaminase and reductase2 involved in riboflavin biosynthesis 34 d1smya1 not modelled 7.3 63 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RNA polymerase alpha subunit dimerisation 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