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Table 1 Proposed template structures obtained from three threading methods along with the calculated scores.

From: Sequence analysis and structure prediction of type II Pseudomonas sp. USM 4–55 PHA synthase and an insight into its catalytic mechanism

Method

Template

Fold

% id

Score

3DPSSM

Human Gastric Lipase (PDB id: 1HLG)

α/β hydrolase fold

11

E valuea = 0.00888

 

Human soluble epoxide hydrolase (PDB id: 1S8O)

α/β hydrolase fold

14

E value = 0.327

 

Bromoperoxidase (PDB id: 1BRT)

α/β hydrolase fold

11

E value = 0.519

mGenThreader

Haloalkane Dehalogenase (PDB id: 1BN6:A)

α/β hydrolase fold

11

E valueb = 3e-05

 

Mouse Epoxide Hydrolase (PDB id: 1CR6:A)

α/β hydrolase fold

8

E value = 3e-05

 

Human Gastric Lipase (PDB id: 1HLG:A)

α/β hydrolase fold

11

E value = 3e-05

FUGUE

Human Gastric Lipase (PDB id: 1HLG:A)

α/β hydrolase fold

11

Z-SCOREc = 7.86

 

Hydroxynitrile-Lyase (PDB id: 1QJ4)

α/β hydrolase fold

11

Z-SCORE = 6.31

 

Proline Iminopeptidase (PDB id: 1AZW)

α/β hydrolase fold

12

Z-SCORE = 5.08

  1. a E-value must be as low as possible
  2. b E-value < 0.001; very significant and certain
  3. c Recommended cutoff : Z-SCORE >= 6.0 (CERTAIN 99% confidence)