GapMind for catabolism of small carbon sources


L-citrulline catabolism in Shewanella oneidensis MR-1

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 SO1043
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component SO1042 SO4655
arcB ornithine carbamoyltransferase SO0277 SO1301
arcC carbamate kinase
odc L-ornithine decarboxylase SO0314 SO4136
puuA glutamate-putrescine ligase SO1268 SO4410
puuB gamma-glutamylputrescine oxidase SO1274 SO1264
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase SO3496 SO4480
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase SO1267
gabT gamma-aminobutyrate transaminase SO1276 SO3497
gabD succinate semialdehyde dehydrogenase SO1275 SO3496
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) SO0618
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) SO0618
astC succinylornithine transaminase SO0617 SO2741
astD succinylglutamate semialdehyde dehydrogenase SO0619 SO3496
astE succinylglutamate desuccinylase SO2338
atoB acetyl-CoA C-acetyltransferase SO1677 SO0020
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase SO1275 SO3496
davT 5-aminovalerate aminotransferase SO1276 SO0617
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SO3088 SO1680
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SO0021 SO3088
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase SO1897 SO1679
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) SO3497 SO0617
patD gamma-aminobutyraldehyde dehydrogenase SO3496 SO4480
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
PRO3 pyrroline-5-carboxylate reductase SO3354
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1 SO1043
PS417_17600 ABC transporter for L-Citrulline, permease component 2
PS417_17605 ABC transporter for L-Citrulline, ATPase component SO1042 SO4655
puo putrescine oxidase
put1 proline dehydrogenase SO3774
putA L-glutamate 5-semialdeyde dehydrogenase SO3774 SO4480
rocA 1-pyrroline-5-carboxylate dehydrogenase SO3774 SO4480
rocD ornithine aminotransferase SO1276 SO0617

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