Secondary structure and disorder prediction

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Sequence		M	T	D	T	D	K	Q	P	T	F	L	F	H	D	Y	E	T	F	G	T	H	P	A	L	D	R	P	A	Q	F	A	A	I	R	T	D	S	E	F	N	V	I	G	E	P	E	V	F	Y	C	K	P	A	D	D	Y	L	P	Q	P
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.
Sequence		G	A	V	L	I	T	G	I	T	P	Q	E	A	R	A	K	G	E	N	E	A	A	F	A	A	R	I	H	S
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 2qxf chain A domain 1 Region: 7 - 88 Aligned: 82 Modelled: 82 Confidence: 100.0% Identity: 99% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 1y97 chain A domain 1 Region: 3 - 87 Aligned: 85 Modelled: 85 Confidence: 99.8% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 2f96 chain A domain 1 Region: 5 - 87 Aligned: 83 Modelled: 83 Confidence: 99.8% Identity: 24% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 3u6f chain A Region: 3 - 87 Aligned: 85 Modelled: 84 Confidence: 99.8% Identity: 22% PDB header:hydrolase/dna Chain: A: PDB Molecule:three prime repair exonuclease 1; PDBTitle: mouse trex1 d200n mutant Phyre2 PDB 3tr8 chain A Region: 5 - 87 Aligned: 82 Modelled: 83 Confidence: 99.8% Identity: 18% PDB header:hydrolase Chain: A: PDB Molecule:oligoribonuclease; PDBTitle: structure of an oligoribonuclease (orn) from coxiella burnetii Phyre2 PDB 1j9a chain A Region: 3 - 88 Aligned: 85 Modelled: 85 Confidence: 99.8% Identity: 19% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 3b6o chain A domain 1 Region: 6 - 87 Aligned: 82 Modelled: 82 Confidence: 99.8% Identity: 22% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 3cm6 chain A Region: 9 - 87 Aligned: 78 Modelled: 79 Confidence: 99.8% Identity: 24% PDB header:hydrolase, apoptosis Chain: A: PDB Molecule:cell death-related nuclease 4; PDBTitle: crystal structure of cell-death related nuclease 4 (crn-4)2 bound with er Phyre2 PDB 1w0h chain A Region: 9 - 88 Aligned: 79 Modelled: 80 Confidence: 99.8% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 2xri chain A Region: 3 - 88 Aligned: 85 Modelled: 86 Confidence: 99.8% Identity: 15% PDB header:hydrolase Chain: A: PDB Molecule:eri1 exoribonuclease 3; PDBTitle: crystal structure of human eri1 exoribonuclease 3 Phyre2 PDB 2gbz chain A Region: 7 - 88 Aligned: 81 Modelled: 82 Confidence: 99.8% Identity: 17% PDB header:hydrolase Chain: A: PDB Molecule:oligoribonuclease; PDBTitle: the crystal structure of xc847 from xanthomonas campestris: a 3-52 oligoribonuclease of dnaq fold family with a novel opposingly-shifted3 helix Phyre2 PDB 2igi chain A domain 1 Region: 4 - 89 Aligned: 85 Modelled: 86 Confidence: 99.8% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 1zbh chain A Region: 9 - 88 Aligned: 79 Modelled: 80 Confidence: 99.7% Identity: 13% PDB header:hydrolase/rna Chain: A: PDB Molecule:3'-5' exonuclease eri1; PDBTitle: 3'-end specific recognition of histone mrna stem-loop by 3'-2 exonuclease Phyre2 PDB 1zbu chain B Region: 9 - 87 Aligned: 78 Modelled: 79 Confidence: 99.7% Identity: 13% PDB header:hydrolase Chain: B: PDB Molecule:3'-5' exonuclease eri1; PDBTitle: crystal structure of full-length 3'-exonuclease Phyre2 PDB 2gui chain A domain 1 Region: 9 - 87 Aligned: 75 Modelled: 79 Confidence: 99.7% Identity: 20% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 2p1j chain B Region: 9 - 87 Aligned: 74 Modelled: 79 Confidence: 99.7% Identity: 23% PDB header:transferase Chain: B: PDB Molecule:dna polymerase iii polc-type; PDBTitle: crystal structure of a polc-type dna polymerase iii2 exonuclease domain from thermotoga maritima Phyre2 PDB 1wlj chain A Region: 9 - 88 Aligned: 72 Modelled: 80 Confidence: 99.5% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 2is3 chain B Region: 5 - 75 Aligned: 52 Modelled: 71 Confidence: 98.3% Identity: 13% PDB header:hydrolase Chain: B: PDB Molecule:ribonuclease t; PDBTitle: crystal structure of escherichia coli rnase t Phyre2 PDB 1uoc chain A Region: 6 - 89 Aligned: 83 Modelled: 84 Confidence: 98.1% Identity: 18% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: CAF1-like ribonuclease Phyre2 PDB 1x9m chain A domain 1 Region: 10 - 38 Aligned: 29 Modelled: 29 Confidence: 97.4% Identity: 7% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 1 d2qxfa1 2 d1y97a1 3 d2f96a1 4 c3u6fA_ 5 c3tr8A_ 6 d1j9aa_ 7 d3b6oa1 8 c3cm6A_ 9 d1w0ha_ 10 c2xriA_ 11 c2gbzA_ 12 d2igia1 13 c1zbhA_ 14 c1zbuB_ 15 d2guia1 16 c2p1jB_ 17 d1wlja_ 18 c2is3B_ 19 d1uoca_ 20 d1x9ma1 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

Detailed template information

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

1 d2qxfa1 100.0 99 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 2 d1y97a1 99.8 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 3 d2f96a1 99.8 24 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 4 c3u6fA_ 99.8 22 PDB header:hydrolase/dna Chain: A: PDB Molecule:three prime repair exonuclease 1; PDBTitle: mouse trex1 d200n mutant 5 c3tr8A_ 99.8 18 PDB header:hydrolase Chain: A: PDB Molecule:oligoribonuclease; PDBTitle: structure of an oligoribonuclease (orn) from coxiella burnetii 6 d1j9aa_ 99.8 19 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 7 d3b6oa1 99.8 22 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 8 c3cm6A_ 99.8 24 PDB header:hydrolase, apoptosis Chain: A: PDB Molecule:cell death-related nuclease 4; PDBTitle: crystal structure of cell-death related nuclease 4 (crn-4)2 bound with er 9 d1w0ha_ 99.8 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 10 c2xriA_ 99.8 15 PDB header:hydrolase Chain: A: PDB Molecule:eri1 exoribonuclease 3; PDBTitle: crystal structure of human eri1 exoribonuclease 3 11 c2gbzA_ 99.8 17 PDB header:hydrolase Chain: A: PDB Molecule:oligoribonuclease; PDBTitle: the crystal structure of xc847 from xanthomonas campestris: a 3-52 oligoribonuclease of dnaq fold family with a novel opposingly-shifted3 helix 12 d2igia1 99.8 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 13 c1zbhA_ 99.7 13 PDB header:hydrolase/rna Chain: A: PDB Molecule:3'-5' exonuclease eri1; PDBTitle: 3'-end specific recognition of histone mrna stem-loop by 3'-2 exonuclease 14 c1zbuB_ 99.7 13 PDB header:hydrolase Chain: B: PDB Molecule:3'-5' exonuclease eri1; PDBTitle: crystal structure of full-length 3'-exonuclease 15 d2guia1 99.7 20 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 16 c2p1jB_ 99.7 23 PDB header:transferase Chain: B: PDB Molecule:dna polymerase iii polc-type; PDBTitle: crystal structure of a polc-type dna polymerase iii2 exonuclease domain from thermotoga maritima 17 d1wlja_ 99.5 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 18 c2is3B_ 98.3 13 PDB header:hydrolase Chain: B: PDB Molecule:ribonuclease t; PDBTitle: crystal structure of escherichia coli rnase t 19 d1uoca_ 98.1 18 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:CAF1-like ribonuclease 20 d1x9ma1 97.4 7 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 21 c2p51A_ not modelled 96.7 23 PDB header:hydrolase, gene regulation Chain: A: PDB Molecule:spcc18.06c protein; PDBTitle: crystal structure of the s. pombe pop2p deadenylation2 subunit 22 d1kfsa1 not modelled 96.4 9 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 23 d2d5ra1 not modelled 96.1 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:CAF1-like ribonuclease 24 d2hhva1 not modelled 96.1 9 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 25 c2kzzA_ not modelled 95.7 19 PDB header:transferase/dna Chain: A: PDB Molecule:protein (dna polymerase i); PDBTitle: klenow fragment with normal substrate and zinc only 26 c1njzA_ not modelled 93.8 8 PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase i; PDBTitle: cytosine-thymine mismatch at the polymerase active site 27 c2a1sC_ not modelled 93.5 25 PDB header:hydrolase Chain: C: PDB Molecule:poly(a)-specific ribonuclease parn; PDBTitle: crystal structure of native parn nuclease domain 28 c1tk0A_ not modelled 92.8 7 PDB header:transferase/electron transport/dna Chain: A: PDB Molecule:dna polymerase; PDBTitle: t7 dna polymerase ternary complex with 8 oxo guanosine and2 ddctp at the insertion site 29 c3d45B_ not modelled 89.5 19 PDB header:hydrolase Chain: B: PDB Molecule:poly(a)-specific ribonuclease parn; PDBTitle: crystal structure of mouse parn in complex with m7gpppg 30 d1wn7a1 not modelled 89.2 22 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 31 d1d5aa1 not modelled 83.9 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 32 d1tgoa1 not modelled 81.0 24 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 33 d1qhta1 not modelled 80.0 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 34 c2gv9B_ not modelled 74.5 12 PDB header:transferase Chain: B: PDB Molecule:dna polymerase; PDBTitle: crystal structure of the herpes simplex virus type 1 dna polymerase 35 d1yt3a3 not modelled 65.2 11 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 36 c3iayA_ not modelled 64.9 18 PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase delta catalytic subunit; PDBTitle: ternary complex of dna polymerase delta 37 c2vwkA_ not modelled 61.4 22 PDB header:dna replication Chain: A: PDB Molecule:dna polymerase; PDBTitle: uracil recognition in archaeal dna polymerases captured by2 x-ray crystallography. v93q polymerase variant 38 c4ktqA_ not modelled 58.8 17 PDB header:transferase/dna Chain: A: PDB Molecule:protein (large fragment of dna polymerase i); PDBTitle: binary complex of the large fragment of dna polymerase i2 from t. aquaticus bound to a primer/template dna 39 c2e6mA_ not modelled 53.9 12 PDB header:hydrolase Chain: A: PDB Molecule:werner syndrome atp-dependent helicase homolog; PDBTitle: structure of mouse werner exonuclease domain 40 c1yt3A_ not modelled 51.0 15 PDB header:hydrolase,translation Chain: A: PDB Molecule:ribonuclease d; PDBTitle: crystal structure of escherichia coli rnase d, an2 exoribonuclease involved in structured rna processing 41 c1d5aA_ not modelled 45.4 20 PDB header:transferase Chain: A: PDB Molecule:protein (dna polymerase); PDBTitle: crystal structure of an archaebacterial dna polymerase2 d.tok. deposition of second native structure at 2.43 angstrom 42 d1ih7a1 not modelled 27.7 20 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 43 c2w0iA_ not modelled 17.6 10 PDB header:transferase Chain: A: PDB Molecule:twinfilin-2; PDBTitle: structure of c-terminal actin depolymerizing factor2 homology (adf-h) domain of human twinfilin-2 44 c2kd5A_ not modelled 13.2 13 PDB header:hormone Chain: A: PDB Molecule:actin severing and dynamics regulatory protein; PDBTitle: solution structure of adf/cofilin (ldcof) from leishmania donovani 45 d1ak7a_ not modelled 11.0 10 Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Cofilin-like 46 c3hhjA_ not modelled 10.7 11 PDB header:hydrolase Chain: A: PDB Molecule:mutator mutt protein; PDBTitle: crystal structure of mutator mutt from bartonella henselae 47 c3cymA_ not modelled 10.6 22 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein bad_0989; PDBTitle: crystal structure of protein bad_0989 from bifidobacterium2 adolescentis 48 c2d3wB_ not modelled 10.2 18 PDB header:biosynthetic protein Chain: B: PDB Molecule:probable atp-dependent transporter sufc; PDBTitle: crystal structure of escherichia coli sufc, an atpase2 compenent of the suf iron-sulfur cluster assembly machinery 49 d2dk8a1 not modelled 9.6 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:RPO3F domain-like 50 c2xfaA_ not modelled 9.3 10 PDB header:protein binding Chain: A: PDB Molecule:actin depolymerization factor 2; PDBTitle: crystal structure of plasmodium berghei actin2 depolymerization factor 2 51 d2hbka2 not modelled 8.5 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 52 c2i2qA_ not modelled 8.4 10 PDB header:actin-binding protein Chain: A: PDB Molecule:cofilin; PDBTitle: fission yeast cofilin 53 d1q8ga_ not modelled 8.1 10 Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Cofilin-like 54 d1q8ia1 not modelled 6.5 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 55 c3iydB_ not modelled 6.5 24 PDB header:transcription/dna Chain: B: PDB Molecule:dna-directed rna polymerase subunit alpha; PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex 56 d1cnua_ not modelled 5.3 10 Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Cofilin-like 57 d1s5ja1 not modelled 5.3 12 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 58 c1s5jA_ not modelled 5.2 20 PDB header:transferase Chain: A: PDB Molecule:dna polymerase i; PDBTitle: insight in dna replication: the crystal structure of dna2 polymerase b1 from the archaeon sulfolobus solfataricus

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