Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	R	Y	H	G	E	F	T	Y	Y	V	Y	Q	Q	S	G	R	Y	F	F	C	K	K	L	T	K	K	R	D	T	S	N	C	N	H	L	H	I	I	R	E	L	S	F	N	E	D	E	L	E	L	I	D	F	S	T	D	G	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																					?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.
Sequence		D	A	N	D	K	E	I	I	R	G	M	I	D	E	L	K	K
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 3nm7 chain C Region: 6 - 18 Aligned: 13 Modelled: 13 Confidence: 12.5% Identity: 31% PDB header:nucleic acid binding protein Chain: C: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of borrelia burgdorferi pur-alpha Phyre2 PDB 3nm7 chain D Region: 6 - 18 Aligned: 13 Modelled: 13 Confidence: 12.0% Identity: 31% PDB header:nucleic acid binding protein Chain: D: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of borrelia burgdorferi pur-alpha Phyre2 PDB 3n8b chain A Region: 6 - 18 Aligned: 13 Modelled: 13 Confidence: 12.0% Identity: 31% PDB header:nucleic acid binding protein Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of borrelia burgdorferi pur-alpha Phyre2 PDB 3n8b chain B Region: 6 - 18 Aligned: 13 Modelled: 13 Confidence: 11.8% Identity: 31% PDB header:nucleic acid binding protein Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of borrelia burgdorferi pur-alpha Phyre2 PDB 2pcj chain B Region: 23 - 77 Aligned: 53 Modelled: 55 Confidence: 11.4% Identity: 17% PDB header:hydrolase Chain: B: PDB Molecule:lipoprotein-releasing system atp-binding protein lold; PDBTitle: crystal structure of abc transporter (aq_297) from aquifex aeolicus2 vf5 Phyre2 PDB 1bjt chain A Region: 51 - 73 Aligned: 23 Modelled: 23 Confidence: 11.2% Identity: 35% PDB header:topoisomerase Chain: A: PDB Molecule:topoisomerase ii; PDBTitle: topoisomerase ii residues 409-1201 Phyre2 PDB 1bjt chain A Region: 51 - 73 Aligned: 23 Modelled: 23 Confidence: 11.2% Identity: 35% Fold: Type II DNA topoisomerase Superfamily: Type II DNA topoisomerase Family: Type II DNA topoisomerase Phyre2 PDB 1l4d chain B Region: 38 - 58 Aligned: 21 Modelled: 21 Confidence: 11.1% Identity: 38% Fold: beta-Grasp (ubiquitin-like) Superfamily: Staphylokinase/streptokinase Family: Staphylokinase/streptokinase Phyre2 PDB 1uw0 chain A Region: 58 - 77 Aligned: 20 Modelled: 20 Confidence: 11.0% Identity: 35% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: PARP-type zinc finger Phyre2 PDB 1l2t chain A Region: 39 - 77 Aligned: 39 Modelled: 39 Confidence: 10.1% Identity: 26% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: ABC transporter ATPase domain-like Phyre2 PDB 1bml chain C domain 1 Region: 44 - 58 Aligned: 15 Modelled: 15 Confidence: 10.0% Identity: 33% Fold: beta-Grasp (ubiquitin-like) Superfamily: Staphylokinase/streptokinase Family: Staphylokinase/streptokinase Phyre2 PDB 3gkx chain B Region: 32 - 71 Aligned: 40 Modelled: 40 Confidence: 10.0% Identity: 13% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative arsc family related protein; PDBTitle: crystal structure of putative arsc family related protein from2 bacteroides fragilis Phyre2 PDB 3qx3 chain B Region: 51 - 73 Aligned: 23 Modelled: 23 Confidence: 10.0% Identity: 30% PDB header:isomerase/dna/isomerase inhibitor Chain: B: PDB Molecule:dna topoisomerase 2-beta; PDBTitle: human topoisomerase iibeta in complex with dna and etoposide Phyre2 PDB 1v43 chain A domain 3 Region: 23 - 76 Aligned: 52 Modelled: 54 Confidence: 9.6% Identity: 19% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: ABC transporter ATPase domain-like Phyre2 PDB 1l4z chain B Region: 38 - 58 Aligned: 21 Modelled: 21 Confidence: 9.5% Identity: 38% Fold: beta-Grasp (ubiquitin-like) Superfamily: Staphylokinase/streptokinase Family: Staphylokinase/streptokinase Phyre2 PDB 2fok chain A domain 4 Region: 50 - 70 Aligned: 21 Modelled: 21 Confidence: 8.7% Identity: 19% Fold: Restriction endonuclease-like Superfamily: Restriction endonuclease-like Family: Restriction endonuclease FokI, C-terminal (catalytic) domain Phyre2 PDB 1sgw chain A Region: 23 - 77 Aligned: 53 Modelled: 55 Confidence: 8.6% Identity: 21% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: ABC transporter ATPase domain-like Phyre2 PDB 3nym chain A Region: 38 - 77 Aligned: 40 Modelled: 37 Confidence: 8.2% Identity: 20% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: the crystal structure of functionally unknown protein from neisseria2 meningitidis mc58 Phyre2 PDB 2wsh chain C Region: 10 - 53 Aligned: 44 Modelled: 44 Confidence: 8.0% Identity: 14% PDB header:hydrolase Chain: C: PDB Molecule:endonuclease ii; PDBTitle: structure of bacteriophage t4 endoii e118a mutant Phyre2 PDB 3d31 chain A domain 2 Region: 40 - 77 Aligned: 38 Modelled: 38 Confidence: 7.8% Identity: 24% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: ABC transporter ATPase domain-like Phyre2 1 c3nm7C_ 2 c3nm7D_ 3 c3n8bA_ 4 c3n8bB_ 5 c2pcjB_ 6 c1bjtA_ 7 d1bjta_ 8 d1l4db_ 9 d1uw0a_ 10 d1l2ta_ 11 d1bmlc1 12 c3gkxB_ 13 c3qx3B_ 14 d1v43a3 15 d1l4zb_ 16 d2foka4 17 d1sgwa_ 18 c3nymA_ 19 c2wshC_ 20 d3d31a2 21 22 23 24 25 26 27 28

Detailed template information

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

1 c3nm7C_ 12.5 31 PDB header:nucleic acid binding protein Chain: C: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of borrelia burgdorferi pur-alpha 2 c3nm7D_ 12.0 31 PDB header:nucleic acid binding protein Chain: D: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of borrelia burgdorferi pur-alpha 3 c3n8bA_ 12.0 31 PDB header:nucleic acid binding protein Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of borrelia burgdorferi pur-alpha 4 c3n8bB_ 11.8 31 PDB header:nucleic acid binding protein Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of borrelia burgdorferi pur-alpha 5 c2pcjB_ 11.4 17 PDB header:hydrolase Chain: B: PDB Molecule:lipoprotein-releasing system atp-binding protein lold; PDBTitle: crystal structure of abc transporter (aq_297) from aquifex aeolicus2 vf5 6 c1bjtA_ 11.2 35 PDB header:topoisomerase Chain: A: PDB Molecule:topoisomerase ii; PDBTitle: topoisomerase ii residues 409-1201 7 d1bjta_ 11.2 35 Fold:Type II DNA topoisomerase Superfamily:Type II DNA topoisomerase Family:Type II DNA topoisomerase 8 d1l4db_ 11.1 38 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 9 d1uw0a_ 11.0 35 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:PARP-type zinc finger 10 d1l2ta_ 10.1 26 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:ABC transporter ATPase domain-like 11 d1bmlc1 10.0 33 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 12 c3gkxB_ 10.0 13 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative arsc family related protein; PDBTitle: crystal structure of putative arsc family related protein from2 bacteroides fragilis 13 c3qx3B_ 10.0 30 PDB header:isomerase/dna/isomerase inhibitor Chain: B: PDB Molecule:dna topoisomerase 2-beta; PDBTitle: human topoisomerase iibeta in complex with dna and etoposide 14 d1v43a3 9.6 19 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:ABC transporter ATPase domain-like 15 d1l4zb_ 9.5 38 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 16 d2foka4 8.7 19 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease FokI, C-terminal (catalytic) domain 17 d1sgwa_ 8.6 21 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:ABC transporter ATPase domain-like 18 c3nymA_ 8.2 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: the crystal structure of functionally unknown protein from neisseria2 meningitidis mc58 19 c2wshC_ 8.0 14 PDB header:hydrolase Chain: C: PDB Molecule:endonuclease ii; PDBTitle: structure of bacteriophage t4 endoii e118a mutant 20 d3d31a2 7.8 24 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:ABC transporter ATPase domain-like 21 c2cs2A_ not modelled 6.8 25 PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase-1; PDBTitle: solution structure of the second zn-finger domain of2 poly(adp-ribose) polymerase-1 22 c1s2xA_ not modelled 6.5 35 PDB header:unknown function Chain: A: PDB Molecule:cag-z; PDBTitle: crystal structure of cag-z from helicobacter pylori 23 d1s2xa_ not modelled 6.5 35 Fold:STAT-like Superfamily:Cag-Z Family:Cag-Z 24 d1vpla_ not modelled 6.3 21 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:ABC transporter ATPase domain-like 25 d1o8ba1 not modelled 6.3 21 Fold:NagB/RpiA/CoA transferase-like Superfamily:NagB/RpiA/CoA transferase-like Family:D-ribose-5-phosphate isomerase (RpiA), catalytic domain 26 d1ueba2 not modelled 6.0 27 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 27 c3rnvA_ not modelled 5.6 36 PDB header:hydrolase Chain: A: PDB Molecule:helper component proteinase; PDBTitle: structure of the autocatalytic cysteine protease domain of potyvirus2 helper-component proteinase 28 d1uura1 not modelled 5.5 17 Fold:STAT-like Superfamily:STAT Family:STAT

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