Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	S	R	R	D	W	Q	L	Q	Q	L	G	I	T	Q	W	S	L	R	R	P	G	A	L	Q	G	E	I	A	I	A	I	P	A	H	V	R	L	V	M	V	A	N	D	L	P	A	L	T	D	P	L	V	S	D	V	L	R	A
Secondary structure
SS confidence
Disorder		?	?	?																							?			?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	T	V	S	P	D	Q	V	L	Q	L	T	P	E	K	I	A	M	L	P	Q	G	S	H	C	N	S	W	R	L	G	T	D	E	P	L	S	L	E	G	A	Q	V	A	S	P	A	L	T	D	L	R	A	N	P	T	A	R	A	A
Secondary structure
SS confidence
Disorder																																		?	?	?	?	?	?	?	?												?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.
Sequence		L	W	Q	Q	I	C	T	Y	E	H	D	F	F	P	R	N	D
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 1em8 chain B Region: 27 - 136 Aligned: 110 Modelled: 110 Confidence: 100.0% Identity: 100% Fold: DNA polymerase III psi subunit Superfamily: DNA polymerase III psi subunit Family: DNA polymerase III psi subunit Phyre2 PDB 3sxu chain B Region: 33 - 134 Aligned: 102 Modelled: 102 Confidence: 100.0% Identity: 100% PDB header:transferase Chain: B: PDB Molecule:dna polymerase iii subunit psi; PDBTitle: structure of the e. coli ssb-dna polymerase iii interface Phyre2 PDB 3gli chain P Region: 2 - 28 Aligned: 27 Modelled: 27 Confidence: 98.4% Identity: 100% PDB header:transferase/dna Chain: P: PDB Molecule:dna polymerase iii subunit psi; PDBTitle: crystal structure of the e. coli clamp loader bound to2 primer-template dna and psi peptide Phyre2 PDB 3gli chain O Region: 2 - 28 Aligned: 27 Modelled: 27 Confidence: 98.4% Identity: 100% PDB header:transferase/dna Chain: O: PDB Molecule:dna polymerase iii subunit psi; PDBTitle: crystal structure of the e. coli clamp loader bound to2 primer-template dna and psi peptide Phyre2 PDB 1ui0 chain A Region: 34 - 72 Aligned: 39 Modelled: 39 Confidence: 24.1% Identity: 18% Fold: Uracil-DNA glycosylase-like Superfamily: Uracil-DNA glycosylase-like Family: Mug-like Phyre2 PDB 1vk2 chain A Region: 34 - 72 Aligned: 39 Modelled: 39 Confidence: 15.4% Identity: 21% Fold: Uracil-DNA glycosylase-like Superfamily: Uracil-DNA glycosylase-like Family: Mug-like Phyre2 PDB 2kbo chain A Region: 43 - 72 Aligned: 30 Modelled: 30 Confidence: 15.1% Identity: 17% PDB header:hydrolase Chain: A: PDB Molecule:dna dc->du-editing enzyme apobec-3g; PDBTitle: structure, interaction, and real-time monitoring of the2 enzymatic reaction of wild type apobec3g Phyre2 PDB 2br6 chain A Region: 12 - 71 Aligned: 60 Modelled: 60 Confidence: 14.7% Identity: 17% PDB header:hydrolase Chain: A: PDB Molecule:aiia-like protein; PDBTitle: crystal structure of quorum-quenching n-acyl homoserine2 lactone lactonase Phyre2 PDB 3mk4 chain A Region: 108 - 125 Aligned: 18 Modelled: 18 Confidence: 12.3% Identity: 17% PDB header:protein transport Chain: A: PDB Molecule:peroxisomal biogenesis factor 3; PDBTitle: x-ray structure of human pex3 in complex with a pex19 derived peptide Phyre2 PDB 1taf chain A Region: 6 - 18 Aligned: 13 Modelled: 13 Confidence: 11.4% Identity: 15% Fold: Histone-fold Superfamily: Histone-fold Family: TBP-associated factors, TAFs Phyre2 PDB 2g80 chain C Region: 51 - 111 Aligned: 61 Modelled: 61 Confidence: 10.9% Identity: 13% PDB header:hydrolase Chain: C: PDB Molecule:protein utr4; PDBTitle: crystal structure of utr4 protein (unknown transcript 4 protein)2 (yel038w) from saccharomyces cerevisiae at 2.28 a resolution Phyre2 PDB 2j8p chain A Region: 67 - 82 Aligned: 16 Modelled: 16 Confidence: 7.7% Identity: 69% PDB header:nuclear protein Chain: A: PDB Molecule:cleavage stimulation factor 64 kda subunit; PDBTitle: nmr structure of c-terminal domain of human cstf-64 Phyre2 PDB 1cmx chain A Region: 46 - 89 Aligned: 44 Modelled: 44 Confidence: 7.0% Identity: 23% Fold: Cysteine proteinases Superfamily: Cysteine proteinases Family: Ubiquitin carboxyl-terminal hydrolase UCH-L Phyre2 PDB 2etl chain A domain 1 Region: 46 - 89 Aligned: 44 Modelled: 44 Confidence: 6.3% Identity: 25% Fold: Cysteine proteinases Superfamily: Cysteine proteinases Family: Ubiquitin carboxyl-terminal hydrolase UCH-L Phyre2 PDB 3o8w chain A Region: 13 - 64 Aligned: 50 Modelled: 52 Confidence: 6.0% Identity: 16% PDB header:signaling protein Chain: A: PDB Molecule:nitrogen regulatory protein p-ii (glnb-1); PDBTitle: archaeoglobus fulgidus glnk1 Phyre2 PDB 2k29 chain A Region: 54 - 76 Aligned: 23 Modelled: 23 Confidence: 5.9% Identity: 30% PDB header:transcription Chain: A: PDB Molecule:antitoxin relb; PDBTitle: structure of the dbd domain of e. coli antitoxin relb Phyre2 PDB 2p5x chain B Region: 2 - 15 Aligned: 14 Modelled: 14 Confidence: 5.6% Identity: 29% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:n-acetylserotonin o-methyltransferase-like protein; PDBTitle: crystal structure of maf domain of human n-acetylserotonin o-2 methyltransferase-like protein Phyre2 1 d1em8b_ 2 c3sxuB_ 3 c3gliP_ 4 c3gliO_ 5 d1ui0a_ 6 d1vk2a_ 7 c2kboA_ 8 c2br6A_ 9 c3mk4A_ 10 d1tafa_ 11 c2g80C_ 12 c2j8pA_ 13 d1cmxa_ 14 d2etla1 15 c3o8wA_ 16 c2k29A_ 17 c2p5xB_

Detailed template information

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

1 d1em8b_ 100.0 100 Fold:DNA polymerase III psi subunit Superfamily:DNA polymerase III psi subunit Family:DNA polymerase III psi subunit 2 c3sxuB_ 100.0 100 PDB header:transferase Chain: B: PDB Molecule:dna polymerase iii subunit psi; PDBTitle: structure of the e. coli ssb-dna polymerase iii interface 3 c3gliP_ 98.4 100 PDB header:transferase/dna Chain: P: PDB Molecule:dna polymerase iii subunit psi; PDBTitle: crystal structure of the e. coli clamp loader bound to2 primer-template dna and psi peptide 4 c3gliO_ 98.4 100 PDB header:transferase/dna Chain: O: PDB Molecule:dna polymerase iii subunit psi; PDBTitle: crystal structure of the e. coli clamp loader bound to2 primer-template dna and psi peptide 5 d1ui0a_ 24.1 18 Fold:Uracil-DNA glycosylase-like Superfamily:Uracil-DNA glycosylase-like Family:Mug-like 6 d1vk2a_ 15.4 21 Fold:Uracil-DNA glycosylase-like Superfamily:Uracil-DNA glycosylase-like Family:Mug-like 7 c2kboA_ 15.1 17 PDB header:hydrolase Chain: A: PDB Molecule:dna dc->du-editing enzyme apobec-3g; PDBTitle: structure, interaction, and real-time monitoring of the2 enzymatic reaction of wild type apobec3g 8 c2br6A_ 14.7 17 PDB header:hydrolase Chain: A: PDB Molecule:aiia-like protein; PDBTitle: crystal structure of quorum-quenching n-acyl homoserine2 lactone lactonase 9 c3mk4A_ 12.3 17 PDB header:protein transport Chain: A: PDB Molecule:peroxisomal biogenesis factor 3; PDBTitle: x-ray structure of human pex3 in complex with a pex19 derived peptide 10 d1tafa_ 11.4 15 Fold:Histone-fold Superfamily:Histone-fold Family:TBP-associated factors, TAFs 11 c2g80C_ 10.9 13 PDB header:hydrolase Chain: C: PDB Molecule:protein utr4; PDBTitle: crystal structure of utr4 protein (unknown transcript 4 protein)2 (yel038w) from saccharomyces cerevisiae at 2.28 a resolution 12 c2j8pA_ 7.7 69 PDB header:nuclear protein Chain: A: PDB Molecule:cleavage stimulation factor 64 kda subunit; PDBTitle: nmr structure of c-terminal domain of human cstf-64 13 d1cmxa_ 7.0 23 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Ubiquitin carboxyl-terminal hydrolase UCH-L 14 d2etla1 6.3 25 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Ubiquitin carboxyl-terminal hydrolase UCH-L 15 c3o8wA_ 6.0 16 PDB header:signaling protein Chain: A: PDB Molecule:nitrogen regulatory protein p-ii (glnb-1); PDBTitle: archaeoglobus fulgidus glnk1 16 c2k29A_ 5.9 30 PDB header:transcription Chain: A: PDB Molecule:antitoxin relb; PDBTitle: structure of the dbd domain of e. coli antitoxin relb 17 c2p5xB_ 5.6 29 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:n-acetylserotonin o-methyltransferase-like protein; PDBTitle: crystal structure of maf domain of human n-acetylserotonin o-2 methyltransferase-like 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