Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	S	G	D	L	V	R	Y	V	I	T	V	M	L	H	E	D	T	L	T	E	I	N	E	L	N	N	Y	L	T	R	D	G	F	L	L	T	M	T	D	D	E	G	N	I	H	E	L	G	T	N	T	F	G	L	I	S	T	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.
Sequence		S	E	E	E	I	R	E	L	V	S	G	L	T	Q	S	A	T	G	K	D	P	E	I	T	I	T	T	W	E	E	W	N	S	N	R	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 1spb chain P Region: 7 - 70 Aligned: 54 Modelled: 55 Confidence: 61.2% Identity: 13% Fold: Ferredoxin-like Superfamily: Protease propeptides/inhibitors Family: Subtilase propeptides/inhibitors Phyre2 PDB 2hiy chain A domain 1 Region: 24 - 91 Aligned: 61 Modelled: 68 Confidence: 35.3% Identity: 20% Fold: SP0830-like Superfamily: SP0830-like Family: SP0830-like Phyre2 PDB 2f5v chain A domain 2 Region: 35 - 83 Aligned: 49 Modelled: 49 Confidence: 22.4% Identity: 10% Fold: FAD-linked reductases, C-terminal domain Superfamily: FAD-linked reductases, C-terminal domain Family: GMC oxidoreductases Phyre2 PDB 2aw0 chain A Region: 11 - 41 Aligned: 30 Modelled: 31 Confidence: 18.4% Identity: 30% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 2bkf chain A domain 1 Region: 3 - 52 Aligned: 50 Modelled: 50 Confidence: 16.2% Identity: 4% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 1ajn chain A Region: 36 - 52 Aligned: 17 Modelled: 17 Confidence: 14.6% Identity: 18% PDB header:antibiotic resistance Chain: A: PDB Molecule:penicillin amidohydrolase; PDBTitle: penicillin acylase complexed with p-nitrophenylacetic acid Phyre2 PDB 3cue chain H Region: 26 - 69 Aligned: 43 Modelled: 44 Confidence: 14.4% Identity: 9% PDB header:protein transport Chain: H: PDB Molecule:transport protein particle 31 kda subunit; PDBTitle: crystal structure of a trapp subassembly activating the rab2 ypt1p Phyre2 PDB 1kn6 chain A Region: 51 - 84 Aligned: 34 Modelled: 34 Confidence: 14.4% Identity: 12% Fold: Ferredoxin-like Superfamily: Protease propeptides/inhibitors Family: Prohormone convertase 1 pro-domain Phyre2 PDB 1cp9 chain A Region: 36 - 52 Aligned: 17 Modelled: 17 Confidence: 12.8% Identity: 18% PDB header:hydrolase Chain: A: PDB Molecule:penicillin amidohydrolase; PDBTitle: crystal structure of penicillin g acylase from the bro12 mutant strain of providencia rettgeri Phyre2 PDB 1gk9 chain A Region: 36 - 52 Aligned: 17 Modelled: 17 Confidence: 12.0% Identity: 18% PDB header:antibiotic resistance Chain: A: PDB Molecule:penicillin g acylase alpha subunit; PDBTitle: crystal structures of penicillin acylase enzyme-substrate2 complexes: structural insights into the catalytic mechanism Phyre2 PDB 3k3w chain A Region: 36 - 52 Aligned: 17 Modelled: 17 Confidence: 11.7% Identity: 24% PDB header:hydrolase Chain: A: PDB Molecule:penicillin g acylase; PDBTitle: thermostable penicillin g acylase from alcaligence faecalis2 in orthorhombic form Phyre2 PDB 1pkx chain A domain 1 Region: 55 - 74 Aligned: 20 Modelled: 20 Confidence: 10.9% Identity: 25% Fold: Methylglyoxal synthase-like Superfamily: Methylglyoxal synthase-like Family: Inosicase Phyre2 PDB 1g8m chain A domain 1 Region: 53 - 74 Aligned: 22 Modelled: 22 Confidence: 10.9% Identity: 18% Fold: Methylglyoxal synthase-like Superfamily: Methylglyoxal synthase-like Family: Inosicase Phyre2 PDB 3kow chain H Region: 27 - 38 Aligned: 12 Modelled: 12 Confidence: 10.8% Identity: 33% PDB header:metal binding protein Chain: H: PDB Molecule:d-ornithine aminomutase s component; PDBTitle: crystal structure of ornithine 4,5 aminomutase backsoaked complex Phyre2 PDB 1oey chain J Region: 13 - 93 Aligned: 71 Modelled: 81 Confidence: 10.1% Identity: 18% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 2kt2 chain A Region: 11 - 42 Aligned: 30 Modelled: 32 Confidence: 10.0% Identity: 17% PDB header:oxidoreductase Chain: A: PDB Molecule:mercuric reductase; PDBTitle: structure of nmera, the n-terminal hma domain of tn501 mercuric2 reductase Phyre2 PDB 3ce8 chain A Region: 3 - 88 Aligned: 78 Modelled: 86 Confidence: 9.4% Identity: 14% PDB header:unknown function Chain: A: PDB Molecule:putative pii-like nitrogen regulatory protein; PDBTitle: crystal structure of a duf3240 family protein (sbal_0098) from2 shewanella baltica os155 at 2.40 a resolution Phyre2 PDB 1s6u chain A Region: 11 - 44 Aligned: 33 Modelled: 34 Confidence: 9.2% Identity: 18% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 1zcz chain A domain 1 Region: 55 - 74 Aligned: 20 Modelled: 20 Confidence: 9.1% Identity: 20% Fold: Methylglyoxal synthase-like Superfamily: Methylglyoxal synthase-like Family: Inosicase Phyre2 PDB 2wyb chain A Region: 36 - 52 Aligned: 17 Modelled: 17 Confidence: 9.1% Identity: 12% PDB header:hydrolase Chain: A: PDB Molecule:acyl-homoserine lactone acylase pvdq subunit PDBTitle: the quorum quenching n-acyl homoserine lactone acylase pvdq2 with a covalently bound dodecanoic acid Phyre2 1 d1spbp_ 2 d2hiya1 3 d2f5va2 4 d2aw0a_ 5 d2bkfa1 6 c1ajnA_ 7 c3cueH_ 8 d1kn6a_ 9 c1cp9A_ 10 c1gk9A_ 11 c3k3wA_ 12 d1pkxa1 13 d1g8ma1 14 c3kowH_ 15 d1oeyj_ 16 c2kt2A_ 17 c3ce8A_ 18 d1s6ua_ 19 d1zcza1 20 c2wybA_ 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

Detailed template information

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

1 d1spbp_ 61.2 13 Fold:Ferredoxin-like Superfamily:Protease propeptides/inhibitors Family:Subtilase propeptides/inhibitors 2 d2hiya1 35.3 20 Fold:SP0830-like Superfamily:SP0830-like Family:SP0830-like 3 d2f5va2 22.4 10 Fold:FAD-linked reductases, C-terminal domain Superfamily:FAD-linked reductases, C-terminal domain Family:GMC oxidoreductases 4 d2aw0a_ 18.4 30 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 5 d2bkfa1 16.2 4 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 6 c1ajnA_ 14.6 18 PDB header:antibiotic resistance Chain: A: PDB Molecule:penicillin amidohydrolase; PDBTitle: penicillin acylase complexed with p-nitrophenylacetic acid 7 c3cueH_ 14.4 9 PDB header:protein transport Chain: H: PDB Molecule:transport protein particle 31 kda subunit; PDBTitle: crystal structure of a trapp subassembly activating the rab2 ypt1p 8 d1kn6a_ 14.4 12 Fold:Ferredoxin-like Superfamily:Protease propeptides/inhibitors Family:Prohormone convertase 1 pro-domain 9 c1cp9A_ 12.8 18 PDB header:hydrolase Chain: A: PDB Molecule:penicillin amidohydrolase; PDBTitle: crystal structure of penicillin g acylase from the bro12 mutant strain of providencia rettgeri 10 c1gk9A_ 12.0 18 PDB header:antibiotic resistance Chain: A: PDB Molecule:penicillin g acylase alpha subunit; PDBTitle: crystal structures of penicillin acylase enzyme-substrate2 complexes: structural insights into the catalytic mechanism 11 c3k3wA_ 11.7 24 PDB header:hydrolase Chain: A: PDB Molecule:penicillin g acylase; PDBTitle: thermostable penicillin g acylase from alcaligence faecalis2 in orthorhombic form 12 d1pkxa1 10.9 25 Fold:Methylglyoxal synthase-like Superfamily:Methylglyoxal synthase-like Family:Inosicase 13 d1g8ma1 10.9 18 Fold:Methylglyoxal synthase-like Superfamily:Methylglyoxal synthase-like Family:Inosicase 14 c3kowH_ 10.8 33 PDB header:metal binding protein Chain: H: PDB Molecule:d-ornithine aminomutase s component; PDBTitle: crystal structure of ornithine 4,5 aminomutase backsoaked complex 15 d1oeyj_ 10.1 18 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 16 c2kt2A_ 10.0 17 PDB header:oxidoreductase Chain: A: PDB Molecule:mercuric reductase; PDBTitle: structure of nmera, the n-terminal hma domain of tn501 mercuric2 reductase 17 c3ce8A_ 9.4 14 PDB header:unknown function Chain: A: PDB Molecule:putative pii-like nitrogen regulatory protein; PDBTitle: crystal structure of a duf3240 family protein (sbal_0098) from2 shewanella baltica os155 at 2.40 a resolution 18 d1s6ua_ 9.2 18 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 19 d1zcza1 9.1 20 Fold:Methylglyoxal synthase-like Superfamily:Methylglyoxal synthase-like Family:Inosicase 20 c2wybA_ 9.1 12 PDB header:hydrolase Chain: A: PDB Molecule:acyl-homoserine lactone acylase pvdq subunit PDBTitle: the quorum quenching n-acyl homoserine lactone acylase pvdq2 with a covalently bound dodecanoic acid 21 d1m32a_ not modelled 9.1 19 Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Cystathionine synthase-like 22 c2dunA_ not modelled 9.1 12 PDB header:transferase Chain: A: PDB Molecule:dna polymerase mu; PDBTitle: solution structure of brct domain of dna polymerase mu 23 c1zr6A_ not modelled 8.9 24 PDB header:oxidoreductase Chain: A: PDB Molecule:glucooligosaccharide oxidase; PDBTitle: the crystal structure of an acremonium strictum glucooligosaccharide2 oxidase reveals a novel flavinylation 24 d1wxia1 not modelled 8.5 13 Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Adenine nucleotide alpha hydrolases-like Family:N-type ATP pyrophosphatases 25 c3q4gA_ not modelled 8.5 15 PDB header:ligase Chain: A: PDB Molecule:nh(3)-dependent nad(+) synthetase; PDBTitle: structure of nad synthetase from vibrio cholerae 26 d1kjqa2 not modelled 8.2 13 Fold:PreATP-grasp domain Superfamily:PreATP-grasp domain Family:BC N-terminal domain-like 27 c3hbxB_ not modelled 7.8 13 PDB header:lyase Chain: B: PDB Molecule:glutamate decarboxylase 1; PDBTitle: crystal structure of gad1 from arabidopsis thaliana 28 c3dpiA_ not modelled 7.3 21 PDB header:ligase Chain: A: PDB Molecule:nad+ synthetase; PDBTitle: crystal structure of nad+ synthetase from burkholderia pseudomallei 29 c3tqxA_ not modelled 7.0 11 PDB header:transferase Chain: A: PDB Molecule:2-amino-3-ketobutyrate coenzyme a ligase; PDBTitle: structure of the 2-amino-3-ketobutyrate coenzyme a ligase (kbl) from2 coxiella burnetii 30 d1d0na4 not modelled 6.9 17 Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Gelsolin-like 31 d1tiba_ not modelled 6.9 6 Fold:alpha/beta-Hydrolases Superfamily:alpha/beta-Hydrolases Family:Fungal lipases 32 c1thzA_ not modelled 6.7 20 PDB header:transferase, hydrolase Chain: A: PDB Molecule:bifunctional purine biosynthesis protein purh; PDBTitle: crystal structure of avian aicar transformylase in complex2 with a novel inhibitor identified by virtual ligand3 screening 33 c2gcfA_ not modelled 6.6 19 PDB header:hydrolase Chain: A: PDB Molecule:cation-transporting atpase pacs; PDBTitle: solution structure of the n-terminal domain of the coppper(i) atpase2 pacs in its apo form 34 c4a1oB_ not modelled 6.5 24 PDB header:transferase-hydrolase Chain: B: PDB Molecule:bifunctional purine biosynthesis protein purh; PDBTitle: crystal structure of mycobacterium tuberculosis purh complexed with2 aicar and a novel nucleotide cfair, at 2.48 a resolution. 35 c2ae3A_ not modelled 6.4 24 PDB header:hydrolase Chain: A: PDB Molecule:glutaryl 7-aminocephalosporanic acid acylase; PDBTitle: glutaryl 7-aminocephalosporanic acid acylase: mutational study of2 activation mechanism 36 d1q5ya_ not modelled 6.3 33 Fold:Ferredoxin-like Superfamily:ACT-like Family:Nickel responsive regulator NikR, C-terminal domain 37 d1wj6a_ not modelled 6.0 4 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 38 d2fg9a1 not modelled 5.9 19 Fold:Split barrel-like Superfamily:FMN-binding split barrel Family:PNP-oxidase like 39 c2jz7A_ not modelled 5.8 23 PDB header:selenium-binding protein Chain: A: PDB Molecule:selenium binding protein; PDBTitle: solution nmr structure of selenium-binding protein from2 methanococcus vannielii 40 c3flpJ_ not modelled 5.7 14 PDB header:sugar binding protein Chain: J: PDB Molecule:sap-like pentraxin; PDBTitle: crystal structure of native heptameric sap-like pentraxin2 from limulus polyphemus 41 c3hqtB_ not modelled 5.5 15 PDB header:transferase Chain: B: PDB Molecule:cai-1 autoinducer synthase; PDBTitle: plp-dependent acyl-coa transferase cqsa 42 c2rmlA_ not modelled 5.4 16 PDB header:hydrolase Chain: A: PDB Molecule:copper-transporting p-type atpase copa; PDBTitle: solution structure of the n-terminal soluble domains of2 bacillus subtilis copa 43 d1scjb_ not modelled 5.4 16 Fold:Ferredoxin-like Superfamily:Protease propeptides/inhibitors Family:Subtilase propeptides/inhibitors 44 d1jmsa4 not modelled 5.4 10 Fold:Nucleotidyltransferase Superfamily:Nucleotidyltransferase Family:DNA polymerase beta-like 45 c3uowB_ not modelled 5.3 14 PDB header:ligase Chain: B: PDB Molecule:gmp synthetase; PDBTitle: crystal structure of pf10_0123, a gmp synthetase from plasmodium2 falciparum 46 c1zczA_ not modelled 5.2 16 PDB header:transferase/hydrolase Chain: A: PDB Molecule:bifunctional purine biosynthesis protein purh; PDBTitle: crystal structure of phosphoribosylaminoimidazolecarboxamide2 formyltransferase / imp cyclohydrolase (tm1249) from thermotoga3 maritima at 1.88 a resolution 47 d2fh1a1 not modelled 5.2 17 Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Gelsolin-like 48 d1kqpa_ not modelled 5.2 18 Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Adenine nucleotide alpha hydrolases-like Family:N-type ATP pyrophosphatases 49 d2o3aa1 not modelled 5.2 33 Fold:alpha/beta knot Superfamily:alpha/beta knot Family:AF0751-like 50 d1r7ma2 not modelled 5.1 24 Fold:Homing endonuclease-like Superfamily:Homing endonucleases Family:Group I mobile intron endonuclease

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