Table 2 Comparison of putative genes related to main pathways for central aromatic catabolism among pseudomonad PGPR

Gene

Product name

GP72 ORF ID MOK_0

Pf-5 ORF ID PFL_

M18 ORF ID PAM18_

A1501 ORF ID PST_

3-oxoadipate (β-ketoadipate) pathway

Catechol degradation III (ortho-cleavage pathway) to 3-oxoadipate enol-lactone

catA

catechol 1, 2-dioxygenase [EC:1.13.11.1]

1630

3860

2532

1674

catC

muconolactone D-isomerase [EC:5.3.3.4]

1631

3861

2531

1673

catB

muconate cycloisomerase [EC:5.5.1.1]

1632

3862

2530

1672

catR

transcriptional regulator [COG0583]

1633

3863

2529

- ^b

Protocatechuate degradation II (ortho-cleavage pathway) to 3-oxoadipate enol-lactone

pcaG

protocatechuate 3,4-dioxygenase, alpha subunit [EC:1.13.11.3]

1264

5395

0155

1250

pcaH

protocatechuate 3,4-dioxygenase, beta subunit [EC:1.13.11.3]

1265

5396

0154

1249

pcaH

protocatechuate 3,4-dioxygenase, beta subunit [EC:1.13.11.4]

1266

5396

0154

1249

pcaQ

LysR family transcriptional regulator, pca operon transcriptional activator [KO:K02623]

1267

5397

0153

1248

pcaH

protocatechuate 3,4-dioxygenase, beta subunit [EC:1.13.11.3]

2952

1320

-

-

pcaG

protocatechuate 3,4-dioxygenase, alpha subunit [EC:1.13.11.3]

2953

1321

-

-

pcaT

MFS transporter, MHS family, dicarboxylic acid transporter PcaT [KO:K02625]

2954

1322

0225

-

pcaB

3-carboxy-cis,cis-muconate cycloisomerase [EC:5.5.1.2]

2955

1323

0226

1257

pcaC

4-carboxymuconolactone decarboxylase [EC:4.1.1.44]

2957

1325

0227

1259

3-Oxoadipate enol-lactone degradation to succinyl-CoA

pcaD

3-oxoadipate enol-lactonase [EC:3.1.1.24]

2956

1324

0226

1258

pcaI

Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [EC:2.8.3.12]

2949

1317

0222

1254

pcaJ

Acyl CoA:acetate/3-ketoacid CoA transferase, beta subunit [EC:2.8.3.12]

2950

1318

0223

1255

pcaR

beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family [K02624]

2946

1315

0156

1253

pcaK

MFS transporter, AAHS family, 4-hydroxybenzoate transporter [KO:K08195]

2947

1316

0231

-

pcaK

MFS transporter, AAHS family, 4-hydroxybenzoate transporter [KO:K08195]

2948

1316

0231

-

pcaF

3-oxoadipyl-CoA thiolase [EC:2.3.1.174]

2951

1319

0224

1256

Homogentisate pathway and catabolism of phenylalanine and tyrosine

L-Phenylalanine degradation

phhA

phenylalanine-4-hydroxylase [EC:1.14.16.1]

1525

1611

4167

3562

Tyrosine degradation I to acetoacetate and fumarate

tyrB

aromatic-amino-acid transaminase [EC:2.6.1.57]

1527

1609

4169

3564

tyrB

aromatic-amino-acid transaminase [EC:2.6.1.57]

3418

2045

1824

2998

hppD

4-hydroxyphenylpyruvate dioxygenase [EC:1.13.11.27]

5394

3387

-

-

hppD

4-hydroxyphenylpyruvate dioxygenase [EC:1.13.11.27]

1257

5385

0238

0200

hmgA

homogentisate 1,2-dioxygenase [EC:1.13.11.5]

2407

0967

3036

-

hmgC

maleylacetoacetate isomerase [EC:5.2.1.2]

2409

0969

3038

-

hmgB

fumarylacetoacetase [EC:3.7.1.2]

2408

0968

3037

-

Tyrosine (4-Hydroxyphenylacetate/3-Hydroxyphenylacetate) degradation II to succinate

hpaC

4-hydroxyphenylacetate-3-hydroxylase small chain [EC:1.14.13.3]

5674

3357

0848

-

hpaB

4-hydroxyphenylacetate-3-hydroxylase large chain [EC:1.14.13.3]

5675

3356

0849

-

hpaD

3,4-dihydroxyphenylacetate 2,3-dioxygenase [EC:1.13.11.15]

5409

3373

0815

-

hpaE

5-carboxymethyl-2-hydroxymuconic-semialdehyde dehydrogenase [EC:1.2.1.60]

5410

3372

0816

-

hpaF

5-carboxymethyl-2-hydroxymuconate isomerase [EC:5.3.3.10]

5528

1486

-

-

hpaF

5-carboxymethyl-2-hydroxymuconate isomerase [EC:5.3.3.10]

5408

3374

0814

-

hpaG

5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase, C-terminal subunit [EC:4.1.1.68]

5411

3371

0817

-

hpaG

5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase, N-terminal subunit [EC:4.1.1.68]

5412

3370

0818

-

hpaA

4-hydroxyphenylacetate catabolism regulatory protein [KO:K02508]

5413

3369

0819

-

hpaH

2-oxo-hept-3-ene-1,7-dioate hydratase [EC:4.2.1.-]

5406

3376

0812

-

hpaI

2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [EC:4.1.2.-]

5405

3377

0811

-

hpaI

2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [EC:4.1.2.-]

2721

-

-

-

gabD

succinate-semialdehyde dehydrogenase (NADP+) [EC:1.2.1.16]

5324

0185

0260

0096

gabD

succinate-semialdehyde dehydrogenase (NADP+) [EC:1.2.1.16]

2687

0185

-

0740

Phenylethylamine degradation II to phenylacetate

peaD

quinohemoprotein amine dehydrogenase, beta subunit [TIGR03907]

1726

4117

-

-

peaC

quinohemoprotein amine dehydrogenase, gamma subunit [pfam08992]

1727

4118

-

-

peaA

quinohemoprotein amine dehydrogenase, alpha subunit [TIGR03908]

1729

4120

-

-

peaE

phenylacetaldehyde dehydrogenase [EC:1.2.1.39]

1734

4130

-

-

peaE

phenylacetaldehyde dehydrogenase [EC:1.2.1.39]

5496

3217

0867

-

Phenylacetyl-CoA pathway

paaF

phenylacetate-CoA ligase [EC:6.2.1.30]

0341

3132

-

-

paaD

acyl-CoA thioesterase [EC:3.1.2.-]

0343

3131

-

-

paaG

phenylacetate-CoA oxygenase, PaaG subunit [KO:K02609]

0340

3133

-

-

paaH

phenylacetate-CoA oxygenase, PaaH subunit [KO:K02610]

0339

3134

-

-

paaI

phenylacetate-CoA oxygenase, PaaI subunit [KO:K02611]

0338

3135

-

-

paaJ

phenylacetate-CoA oxygenase, PaaJ subunit [KO:K02612]

0337

3136

-

-

paaK

phenylacetate-CoA oxygenase, PaaK subunit [KO:K02613]

0336

3137

-

-

paaN

MaoC_dehydratas/NAD-dependent aldehyde dehydrogenases [KO:K02618]

0332

3140

-

-

paaE

3-oxoadipyl-CoA thiolase [EC:2.3.1.16]

0342

1319

0224

1256

paaB

enoyl-CoA hydratase [EC:4.2.1.17]

0345

3130

-

-

paaA

enoyl-CoA hydratase [EC:4.2.1.17]

0346

-

-

-

paaC

3-hydroxybutyryl-CoA dehydrogenase [EC:1.1.1.157]

0344

-

-

-

paaY

phenylacetic acid degradation protein PaaY [KO:K08279]

0347

3129

-

-

paaX

phenylacetic acid degradation operon negative regulatory protein PaaX [KO:K02616]

0348

3128

-

-