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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.