GapMind for catabolism of small carbon sources


L-citrulline catabolism in Shewanella amazonensis SB2B

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD

Also see fitness data for the top candidates


Overview: Citrulline can be catabolized via ornithine carbamoyltransferase in reverse (PMID:3129535). Genetic evidence suggests that some bacteria use a putative citrullinase (EC to consume citrulline.

51 steps (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component
AO353_03050 ABC transporter for L-Citrulline, permease component 1
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component Sama_1486 Sama_1333
arcB ornithine carbamoyltransferase Sama_0258 Sama_0840
arcC carbamate kinase
odc L-ornithine decarboxylase Sama_3334 Sama_0410
puuA glutamate-putrescine ligase Sama_2644 Sama_1174
puuB gamma-glutamylputrescine oxidase Sama_2638 Sama_2647
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Sama_2648 Sama_3435
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Sama_0794 Sama_2645
gabT gamma-aminobutyrate transaminase Sama_2643 Sama_2636
gabD succinate semialdehyde dehydrogenase Sama_2637 Sama_2648
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) Sama_3010 Sama_1627
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) Sama_3010 Sama_1627
astC succinylornithine transaminase Sama_1628 Sama_3011
astD succinylglutamate semialdehyde dehydrogenase Sama_3009 Sama_1626
astE succinylglutamate desuccinylase Sama_1708
atoB acetyl-CoA C-acetyltransferase Sama_1375 Sama_0031
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase Sama_2637 Sama_2648
davT 5-aminovalerate aminotransferase Sama_2636 Sama_1628
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Sama_1378 Sama_0032
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Sama_0032 Sama_2167
gcdG succinyl-CoA:glutarate CoA-transferase Sama_3300
gcdH glutaryl-CoA dehydrogenase Sama_2796 Sama_1362
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
oraE D-ornithine 4,5-aminomutase, beta (E) subunit
oraS D-ornithine 4,5-aminomutase, alpha (S) subunit
ord 2,4-diaminopentanoate dehydrogenase
orr ornithine racemase
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) Sama_2643 Sama_2649
patD gamma-aminobutyraldehyde dehydrogenase Sama_2648 Sama_3435
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Sama_1530 Sama_1532
PRO3 pyrroline-5-carboxylate reductase Sama_2478
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1
PS417_17600 ABC transporter for L-Citrulline, permease component 2
PS417_17605 ABC transporter for L-Citrulline, ATPase component Sama_2641 Sama_3467
puo putrescine oxidase
put1 proline dehydrogenase Sama_2676
putA L-glutamate 5-semialdeyde dehydrogenase Sama_2676 Sama_2637
rocA 1-pyrroline-5-carboxylate dehydrogenase Sama_2676 Sama_2637
rocD ornithine aminotransferase Sama_2636 Sama_2643

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.



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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory