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Table 5 Comparison of the functional gene counts in the function profile of genome sequences

From: Draft genome sequence of Mycobacterium rufum JS14T, a polycyclic-aromatic-hydrocarbon-degrading bacterium from petroleum-contaminated soil in Hawaii

Function ID

Name

M. van a

M. gil GCKa

M. gil Sp1a

M. aro b

M. ruf b

KO:K00448

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

1

1

1

1

3

KO:K00449

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

1

1

1

1

2

KO:K18253

phthalate 3,4-dioxygenase ferredoxin subunit (phtAc)

0

2

1

2

1

KO:K18254

phthalate 3,4-dioxygenase ferredoxin reductase subunit [EC:1.18.1.3] (phtAd)

1

2

1

0

1

KO:K00517

E1.14.-.- (cytochrome P450)

12

10

10

5

6

KO:K18256

3,4-dihydroxyphthalate decarboxylase [EC:4.1.1.69] (phtC)

1

2

1

0

1

KO:K11943

PAH dioxygenase large subunit [EC:1.13.11.-] (nidA)

1

2

1

1

0

KO:K11944

PAH dioxygenase small subunit [EC:1.13.11.-] (nidB)

2

4

2

4

0

KO:K11948

1-hydroxy-2-naphthoate dioxygenase [EC:1.13.11.38] (phdI)

1

2

1

0

0

KO:K11949

4-(2-carboxyphenyl)-2-oxobut-3-enoate aldolase [EC:4.1.2.34] (phdJ)

1

2

1

1

0

KO:K18251

phthalate 3,4-dioxygenase alpha subunit [EC:1.14.12.-] (phtAa)

1

2

1

0

0

KO:K18252

phthalate 3,4-dioxygenase beta subunit [EC:1.14.12.-] (phtAb)

1

2

1

1

0

KO:K18255

phthalate 3,4-cis-dihydrodiol dehydrogenase [EC:1.3.1.-] (phtB)

1

2

1

1

0

KO:K18257

cis-3,4-dihydrophenanthrene-3,4-diol dehydrogenase [EC:1.3.1.49] (phdE)

1

2

1

1

0

KO:K18275

2-formylbenzoate dehydrogenase [EC:1.2.1.78] (phdK)

1

1

1

1

0

  1. Comparison of the selected five genome sequences was conducted using function profile categories in the IMG-ER pipeline [27], and the genome sequences analyzed are as follows: M. van, M. vanbaalenii PYR-1 (IMG Genome ID 639633044) [6]; M. gil GCK, M. gilvum PYR-GCK (IMG Genome ID 640427122) [8]; M. gil Sp1, M. gilvum Spyr1 IMG Genome ID 649633070) [7]; M. aro, M. aromaticivorans JS19b1 (whole Genome Sequencing) (IMG Genome ID 2558309009) [9]; M. ruf, M. rufum JS14 (whole Genome Sequencing) (IMG Genome ID 2593339261)
  2. Reported sequencing status for the individual genome set: a Complete genome sequence; b Draft whole-genome sequence