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Table 1 BLAST filtering criteria

From: Deciphering chemotaxis pathways using cross species comparisons

Protein

Query sequence length

Max hit length

Domains†

Domains in E. coli from CDART[39]

BLAST 'query from' criteria

BLAST 'query to' criteria

CheA‡

654

-

All

1-654

<400

>610

   

P4

370-505

>340 & <400

>475 & <535

   

P5

509-640

>480 & <540

>610

CheB

349

450

All

1-349

<30

>310

   

1

7-108

<30

>90 & <160

   

2

158-340

>130 & <190

>310

CheR

286

415

All

1-286

<40

>250

   

1

23-78

<50

>50 & <110

   

2

92-283

>60 & <210

>250

CheW§

167

240

All

1-167

-

-

CheY

129

176

All

1-129

<30

>100

CheV*

303

400

All

1-303

<40

>250

   

1

16-153

<40

>120 & <200

   

2

178-301

>140 & <210

>250

CheZ

214

300

All

1-214

<30

>180

  1. †If more than one domain is present in the query sequence, hits with multiple HSPs in the BLAST output were checked to see if each domain was found separately, using the criteria listed.
  2. ‡CheA homologues had to contain at least domains P4 and P5. Note that this means CheA3 from R. sphaeroides is rejected, as it only contains domains P1 and P5.
  3. §No query from or query to restrictions were set for CheW, as this led to the rejection of too many true CheW homologues.
  4. *Query sequence was from Bacillus subtilis
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BMC Systems Biology

ISSN: 1752-0509

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