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Table 1 Predicted core Crc regulon of Pseudomonas.

From: Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

Gene name

Function

PAO1

PA14

PA7

LESB58

Pf0-1

Pf-5

SBW25

KT2440

F1

W619

B728a

DC3000

 
 

Amino acid transport and metabolism

             

putP

Sodium/proline symporter

0783

54150

4736

45601

0453

0496

0452

4946

4818

0522

NM

NM

 
 

Probable amino acid permease

0789

54040

4729

45531

4561

4906

1103

1059

1100

1089

NO

NO

 

phhA

Phenylalanine-4-hydroxylase

0872

52990

4644

44441

1499

1611

4458

4490

1424

3779

NM

NM

Y

gltI

Probable binding protein component of ABC transporter

1342

46910

4043

38391

4535

4871

1139

1071

1112

1100

NM

NM

 
 

Probable sodium/alanine symporter

2252

35460

2989

30521

NM

NM

NM

0496

0530

0551

5052

5500

 
 

Probable glutamine synthetase

2040

38140

3247

32821

5408

5930

5849

5184

5091

0279

4868

5310

 
 

Carbohydrate transport and metabolism

             

mltE

Probable binding protein component of ABC maltose/mannitol transporter

2338

34420

2925

29651

2640

3070

2745

NO

NO

2041

2440

2707

 

oprB

Glucose/carbohydrate outer membrane porin precursor

3186

23030

1943

18821

4366

4613

4842

1019

1057

4205

1117

1296

Y

 

Probable binding protein component of ABC sugar transporter

3190

22980

1939

18781

4370

4617

4846

1015

1053

4209

1113

1292

Y

lldP

L-lactate permease

4770

63080

5490

51551

0753

0817

5278

4735

4601

0696

NO

NO

 

fruA

PTS fructose IIC component

NM

NM

NM

NM

0795

0861

0806

0795

0818

4398

0823

0956

Y

glpF

Glycerol uptake facilitator protein

NM

NM

NM

NM

4531

4867

1143

1076

1117

1105

3904

4167

 
 

Energy production and conservation

             

coxB

Cytochrome c oxidase, subunit II

0105

01290

0180

01061

0079

0061

0058

0103

0119

0122

NO

NO

 

pntB

Pyridine nucleotide transhydrogenase, beta subunit

0196

02470

0277

01971

0112

0113

0111

0155

0173

5072

NM

NO

 

acsA

Acetyl-coenzyme A synthetase

0887

52800

4627

44291

4293

4522

4766

4487

1428

3776

3572

1825

 
 

Putative glycerate 2-kinase

1499

45030

3833

39131

1595

1698

1800

4300

1569

3625

NO

NO

 
 

Probable D-beta-hydroxybutyrate permease

2004

38580

3285

33191

3078

3575

2629

3074

2650

2717

NO

NO

 
 

Putative acetate transporter

3235

22340

1890

18321

1607

1711

1813

1742

3977

1292

3757

1623

 

cstA

Probable carbon starvation protein

4606

60950

5246

49911

4883

5352

5333

4641

4503

0798

4273

4638

 

phaC1

Poly(3-hydroxyalkanoic acid) synthase 1

5056

66820

5794

54461

0394

0434

0396

5003

4877

0461

NO

NO

 

phaF

polyhydroxyalkanoate synthesis protein PhaF

5060

66875

5799

54501

NM

NM

NM

5007

4881

0457

0391

5147

 
 

Alginate metabolism

             

algP

Alginate regulatory protein

5253

69370

5998

56471

NM

NM

NM

0194

0215

0263

0054

0136

 
 

Lipid metabolism

             

fadD2

Long-chain-fatty-acid--CoA ligase

3300

21340

1824

17661

4354

4599

4830

4550

1339

3845

3836

4098

 

estA

Esterase

5112

67510

5845

55021

NM

NM

NM

0418

0452

4784

4606

0569

 
 

Polyamine metabolism

             

aphA

Acetylpolyamine aminohydrolase

1409

46230

3930

40041

5631

6145

6061

5340

5249

0133

NO

NO

 
 

Xenobiotic degradation and transport

             

pcaK

Benzoate transport

NM

NM

NM

NM

1266

1316

1362

1376

4347

1016

2124

2340

 
 

DNA replication, recombination and repair

             

recA

RecA protein

3617

17530

1523

14181

1175

1231

1189

1629

4088

4030

1378

4033

 

hupA

HU family DNA-binding protein

5348

70600

6125

57431

5600

6102

6032

5313

5222

0160

NM

NM

Y

 

nucleotide transport and metabolism

             
 

Probable transporter

1519

44800

3815

38911

1711

4364

4355

4284

1584

3610

NO

NO

 

xdhA

Xanthine dehydrogenase

1524

44710

3809

38041

1797

1889

4592

4278

1590

3604

NM

NM

 
 

Translation

             

rplR

50S ribosomal protein L18

4247

09010

0853

06811

5063

5566

5511

0470

0503

4733

4532

0642

 

tufB

Elongation factor Tu

4277

08830

0835

06631

5081

5584

5529

0452

0485

4751

4550

0624

 
 

Unknown function

             
 

Hypothetical protein

0754

54540

4766

45891

NM

NM

NM

1418

4303

1058

3966

4232

Y

 

Probable transporter

1507

44950

3824

39041

1701

4371

4364

4290

1578

3616

NO

NO

 
 

Probable major facilitator superfamily (MFS) transporter

3709

16410

1427

12731

3359

2486

2159

0057

0073

0076

NO

NO

 
 

Hypothetical protein

3923

13130

1184

10541

4708

5116

0923

0765

0792

4424

0991

1149

 
 

Probable ATP-binding component of ABC transporter

4461

57930

5034

48401

0858

0916

0883

0953

0992

4262

4146

4452

 
 

Hypothetical protein

4570

60480

5210

49531

4863

5332

5174

0685

0716

4500

NO

NO

 
 

Hypothetical protein

5052

66760

5789

54421

0398

0438

0400

5090

4963

0375

NM

NM

 
 

Phosphotransferase domain-containing protein

NM

NM

NM

NM

1487

1597

4880

4500

1412

3789

3586

1810

 
  1. Loci with an A-rich motif in the upstream region in all strains tested for at least three species are shown. The numbers under strain names indicate the locus id, according to Genbank annotation, of the locus with the A-rich motif in the upstream region. NO (no ortholog) indicates that no orthologous locus was found. NM (no motif) indicates that the orthologous locus did not have the A-rich motif in the upstream region. Y indicates that the locus is has increased transcript and/or protein levels in a crc mutant of P. putida KT2442 (a spontaneous rifampicin resistant mutant of KT2440) [26].