Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	V	A	R	F	S	C	G	K	T	A	Q	L	S	K	K	Q	T	G	Y	Y	S	P	E	I	F	P	S	T	G	K	D	C	N	P	Q	P	A	N	C	L	K	D	Q	Y	V	L	R	H	C	C	V	D	D	R	S	G	K	M
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?				?	?	?	?	?	?	?	?	?	?																?		?				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.
Sequence		G	Y	S	V	K	F	L	V	L	T	R	M	D	T	E	T	A	S	L	F	H	C	K	P	C	Y	S	K	M	T	F	T	I	Y	H	P	L	T	H	S	F	F	T	S	C	W
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 2k2w chain A Region: 26 - 37 Aligned: 12 Modelled: 12 Confidence: 33.7% Identity: 50% PDB header:cell cycle Chain: A: PDB Molecule:recombination and dna repair protein; PDBTitle: second brct domain of nbs1 Phyre2 PDB 1twf chain J Region: 6 - 52 Aligned: 33 Modelled: 33 Confidence: 17.2% Identity: 36% Fold: DNA/RNA-binding 3-helical bundle Superfamily: RNA polymerase subunit RPB10 Family: RNA polymerase subunit RPB10 Phyre2 PDB 3czb chain A Region: 19 - 33 Aligned: 15 Modelled: 15 Confidence: 16.0% Identity: 20% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative transglycosylase; PDBTitle: crystal structure of putative transglycosylase from caulobacter2 crescentus Phyre2 PDB 2pmz chain N Region: 6 - 52 Aligned: 32 Modelled: 32 Confidence: 13.0% Identity: 41% PDB header:translation, transferase Chain: N: PDB Molecule:dna-directed rna polymerase subunit n; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus Phyre2 PDB 2pnw chain A domain 1 Region: 19 - 33 Aligned: 15 Modelled: 15 Confidence: 12.9% Identity: 40% Fold: Double psi beta-barrel Superfamily: Barwin-like endoglucanases Family: MLTA-like Phyre2 PDB 2g5d chain A domain 1 Region: 19 - 33 Aligned: 15 Modelled: 15 Confidence: 11.3% Identity: 33% Fold: Double psi beta-barrel Superfamily: Barwin-like endoglucanases Family: MLTA-like Phyre2 PDB 2pi8 chain A domain 1 Region: 7 - 33 Aligned: 27 Modelled: 26 Confidence: 10.7% Identity: 26% Fold: Double psi beta-barrel Superfamily: Barwin-like endoglucanases Family: MLTA-like Phyre2 PDB 2ae0 chain X domain 1 Region: 19 - 33 Aligned: 15 Modelled: 15 Confidence: 10.3% Identity: 40% Fold: Double psi beta-barrel Superfamily: Barwin-like endoglucanases Family: MLTA-like Phyre2 PDB 3cqy chain A Region: 38 - 61 Aligned: 24 Modelled: 24 Confidence: 8.9% Identity: 29% PDB header:transferase Chain: A: PDB Molecule:anhydro-n-acetylmuramic acid kinase; PDBTitle: crystal structure of a functionally unknown protein (so_1313) from2 shewanella oneidensis mr-1 Phyre2 PDB 1niy chain A Region: 31 - 43 Aligned: 13 Modelled: 13 Confidence: 8.6% Identity: 54% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: omega toxin-like Family: Spider toxins Phyre2 PDB 1mb6 chain A Region: 31 - 43 Aligned: 13 Modelled: 13 Confidence: 8.3% Identity: 46% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: omega toxin-like Family: Spider toxins Phyre2 PDB 1b8t chain A domain 4 Region: 82 - 88 Aligned: 7 Modelled: 7 Confidence: 7.5% Identity: 71% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 1b8t chain A domain 2 Region: 82 - 88 Aligned: 7 Modelled: 7 Confidence: 7.5% Identity: 71% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 2djf chain A domain 1 Region: 38 - 47 Aligned: 10 Modelled: 10 Confidence: 7.1% Identity: 40% Fold: Streptavidin-like Superfamily: Dipeptidyl peptidase I (cathepsin C), exclusion domain Family: Dipeptidyl peptidase I (cathepsin C), exclusion domain Phyre2 PDB 1mwp chain A Region: 6 - 43 Aligned: 36 Modelled: 38 Confidence: 7.0% Identity: 25% Fold: SRCR-like Superfamily: A heparin-binding domain Family: A heparin-binding domain Phyre2 PDB 1n93 chain X Region: 47 - 52 Aligned: 6 Modelled: 6 Confidence: 6.8% Identity: 50% PDB header:viral protein Chain: X: PDB Molecule:p40 nucleoprotein; PDBTitle: crystal structure of the borna disease virus nucleoprotein Phyre2 PDB 1n93 chain X Region: 47 - 52 Aligned: 6 Modelled: 6 Confidence: 6.8% Identity: 50% Fold: P40 nucleoprotein Superfamily: P40 nucleoprotein Family: P40 nucleoprotein Phyre2 PDB 1jxc chain A Region: 20 - 29 Aligned: 10 Modelled: 10 Confidence: 6.7% Identity: 50% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Plant defensins Phyre2 PDB 1jqp chain A domain 1 Region: 38 - 47 Aligned: 10 Modelled: 10 Confidence: 6.4% Identity: 40% Fold: Streptavidin-like Superfamily: Dipeptidyl peptidase I (cathepsin C), exclusion domain Family: Dipeptidyl peptidase I (cathepsin C), exclusion domain Phyre2 PDB 3qbw chain A Region: 38 - 61 Aligned: 24 Modelled: 24 Confidence: 6.2% Identity: 29% PDB header:transferase Chain: A: PDB Molecule:anhydro-n-acetylmuramic acid kinase; PDBTitle: crystal structure of pseudomonas aeruginosa 1,6-anhydro-n-2 actetylmuramic acid kinase (anmk) bound to adenosine diphosphate Phyre2 1 c2k2wA_ 2 d1twfj_ 3 c3czbA_ 4 c2pmzN_ 5 d2pnwa1 6 d2g5da1 7 d2pi8a1 8 d2ae0x1 9 c3cqyA_ 10 d1niya_ 11 d1mb6a_ 12 d1b8ta4 13 d1b8ta2 14 d2djfa1 15 d1mwpa_ 16 c1n93X_ 17 d1n93x_ 18 d1jxca_ 19 d1jqpa1 20 c3qbwA_ 21 22 23

Detailed template information

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

1 c2k2wA_ 33.7 50 PDB header:cell cycle Chain: A: PDB Molecule:recombination and dna repair protein; PDBTitle: second brct domain of nbs1 2 d1twfj_ 17.2 36 Fold:DNA/RNA-binding 3-helical bundle Superfamily:RNA polymerase subunit RPB10 Family:RNA polymerase subunit RPB10 3 c3czbA_ 16.0 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative transglycosylase; PDBTitle: crystal structure of putative transglycosylase from caulobacter2 crescentus 4 c2pmzN_ 13.0 41 PDB header:translation, transferase Chain: N: PDB Molecule:dna-directed rna polymerase subunit n; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 5 d2pnwa1 12.9 40 Fold:Double psi beta-barrel Superfamily:Barwin-like endoglucanases Family:MLTA-like 6 d2g5da1 11.3 33 Fold:Double psi beta-barrel Superfamily:Barwin-like endoglucanases Family:MLTA-like 7 d2pi8a1 10.7 26 Fold:Double psi beta-barrel Superfamily:Barwin-like endoglucanases Family:MLTA-like 8 d2ae0x1 10.3 40 Fold:Double psi beta-barrel Superfamily:Barwin-like endoglucanases Family:MLTA-like 9 c3cqyA_ 8.9 29 PDB header:transferase Chain: A: PDB Molecule:anhydro-n-acetylmuramic acid kinase; PDBTitle: crystal structure of a functionally unknown protein (so_1313) from2 shewanella oneidensis mr-1 10 d1niya_ 8.6 54 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Spider toxins 11 d1mb6a_ 8.3 46 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Spider toxins 12 d1b8ta4 7.5 71 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 13 d1b8ta2 7.5 71 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 14 d2djfa1 7.1 40 Fold:Streptavidin-like Superfamily:Dipeptidyl peptidase I (cathepsin C), exclusion domain Family:Dipeptidyl peptidase I (cathepsin C), exclusion domain 15 d1mwpa_ 7.0 25 Fold:SRCR-like Superfamily:A heparin-binding domain Family:A heparin-binding domain 16 c1n93X_ 6.8 50 PDB header:viral protein Chain: X: PDB Molecule:p40 nucleoprotein; PDBTitle: crystal structure of the borna disease virus nucleoprotein 17 d1n93x_ 6.8 50 Fold:P40 nucleoprotein Superfamily:P40 nucleoprotein Family:P40 nucleoprotein 18 d1jxca_ 6.7 50 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Plant defensins 19 d1jqpa1 6.4 40 Fold:Streptavidin-like Superfamily:Dipeptidyl peptidase I (cathepsin C), exclusion domain Family:Dipeptidyl peptidase I (cathepsin C), exclusion domain 20 c3qbwA_ 6.2 29 PDB header:transferase Chain: A: PDB Molecule:anhydro-n-acetylmuramic acid kinase; PDBTitle: crystal structure of pseudomonas aeruginosa 1,6-anhydro-n-2 actetylmuramic acid kinase (anmk) bound to adenosine diphosphate 21 c3eudE_ not modelled 5.4 42 PDB header:nuclear protein Chain: E: PDB Molecule:protein shq1; PDBTitle: structure of the cs domain of the essential h/aca rnp2 assembly protein shq1p 22 c2k8qA_ not modelled 5.2 42 PDB header:structural protein Chain: A: PDB Molecule:protein shq1; PDBTitle: nmr structure of shq1p n-terminal domain 23 d1x4ka1 not modelled 5.2 71 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM 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