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Table 13 Presence of genes in the Synechocystis sp. PCC 6803 genome encoding putative enzymes of an L-arginine decarboxylase-, an L-arginine deiminase-, and an L-arginine oxidase/dehydrogenase pathway.

From: Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

L-arginine-degrading pathways in Synechocystis sp. PCC 6803

ORF

Database #

Length (aa)

pI

MW (kDa)

Best hit vs. gene

Organism

E-value

Similarity (ident./pos. aa)

L-Arginine decarboxylase

L-Arginine decarboxylase (A1)

sll1683

NP_440109

483

5.44

51.84

speA

B. subtilis

5.0e-103

40/61

 

slr0662

NP_442871

695

5.08

78.24

speA

X. campestris

2.0e-134

41/56

 

slr1312

NP_439907

659

5.30

74.48

speA

X. campestris

5.0e-121

38/56

Agmatinase (A2.1)

sll1077

NP_440618

390

5.06

42.96

speB2

P. aeruginosa

1.1e-40

33/41

 

sll0228

NP_440030

306

4.90

33.46

speB

B. subtilis

1.6e-22

30/45

Putrescine oxidase or transaminase (A3)

n.d.

n.d.

n.d.

n.d.

n.d.

n.d.

n.d.

n.d.

n.d.

4-Aminobutyraldehyde dehydrogenase (A4)

sll1495

NP_442886

397

8.43

43.54

BMEII0291

B. melitensis

1.2e-93

42/61

4-Aminobutyrate transaminase (A5)

slr1022

NP_440479

429

5.11

46.54

gabT

P. aeruginosa

6.7e-58

33/50

 

sll0017

NP_442115

433

5.13

45.87

gabT

E. coli

5.7e-41

30/44

Succinate semialdehyde dehydrogenase (A6)

slr0370

NP_442020

454

5.02

48.75

gabD

X. campestris

5.0e-121

47/65

 

sll1561

NP_441689

990

5.46

110.03

gabD

P. aeruginosa

2.7e-66

17/25

L-Arginine deiminase

L-Arginine deiminase (D1)

sll1336

NP_442829

705

5.40

78.33

cyb_250

S. yellowstone

0.0

61/79

L-Ornithine transcarbamoylase (D2)

sll0902

slr1476

NP_442776

NP_441572

308

331

5.38

6.53

33.62

33.39

argF

argF

P. aeruginosa

P. aeruginosa

1.1e-77

7.2e-13

47/66

26/42

Carbamate kinase (D3)

sll0573

NP_443041

308

5.66

32.93

ygcA

E. coli

8.1e-52

41/58

L-Ornithine transaminase (D4)

slr1022

NP_440479

429

5.11

46.54

rocD

B. subtilis

2.1e-61

32/52

Δ1Pyrroline-5-carboxylate dehydrogenase (D5)

slr0370

NP_442020

454

5.02

48.75

ycgN

B. subtilis

7.9e-40

26/40

Δ1Pyrroline-5-carboxylate reductase

slr0661

NP_442689

128

5.11

14.4

slr0661

S. PCC 6803

0.0

100/100

Proline oxidase

sll1561

NP_441689

990

5.46

110.03

rocA

B. subtilis

6.0e-138

25/34

L-Arginine oxidase/dehydrogenase

L-Arginine oxidase/dehydrogenase (E1)

slr0782

NP_442072

471

5.19

51.37

aoxA

S. elongatus

1.7e-18

20/35

4-Guanidino butyrase (E2)

sll1077

NP_440618

390

5.06

42.96

gbuA

P. aeruginosa

1.1e-40

26/41

 

sll0228

NP_440030

306

4.90

33.46

gbuA

P. aeruginosa

1.1e-19

26/41

4-Aminobutyrate transaminase (E3)

slr1022

NP_440479

429

5.11

46.54

gabT

P. aeruginosa

6.7e-58

33/50

 

sll0017

NP_442115

433

5.13

45.87

gabT

P. aeruginosa

5.7e-41

30/44

Succinate semialdehyde dehydrogenase (E4)

slr0370

NP_442020

454

5.02

48.75

gabD

X. campestris

5.0e-121

47/65

 

sll1561

NP_441689

990

5.46

110.03

gabD

P. aeruginosa

2.7e-66

17/25

  1. The letters with numbers in parenthesis behind the enzyme names correspond to those given in Tables 3 and 4, and Fig. 2. In Synechocystis sp. PCC 6803 the gene slr1022 has similarity to L-ornithine transaminases and to 4-aminobutyrate transaminases. The L-ornithine transferase (D2) and the 4-aminobutyrate transferase (E3) both belong to the group of class III aminotransferases (InterProScan), which explains why the same gene slr1022 is annotated either as L-ornithine transaminase or as 4-aminobutyrate transaminase. The gene slr0370 has similarity to the Δ1pyrroline-5-carboxylate dehydrogenase (D5) and to succinate semialdehyde dehydrogenase (E4). Both enzymes belong to the NAD-dependent aldehyde dehydrogenases (InterProScan), which explains why the same gene slr0370 is either annotated as Δ1pyrroline-5-carboxylate dehydrogenase or succinate semialdehyde dehydrogenase Thus, it can not be decided in a bioinformatic approach whether the gene products Slr1022 and Slr0370 are components of the L-arginine deiminase pathway or the L-arginine oxidase/dehydrogenase pathway or of both pathways. N.d. = not detected.
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BMC Genomics

ISSN: 1471-2164

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