GapMind for catabolism of small carbon sources


L-citrulline catabolism in Marinobacter adhaerens HP15

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component HP15_3031
AO353_03050 ABC transporter for L-Citrulline, permease component 1 HP15_3032 HP15_2919
AO353_03045 ABC transporter for L-Citrulline, permease component 2 HP15_3033 HP15_3032
AO353_03040 ABC transporter for L-Citrulline, ATPase component HP15_3030 HP15_2920
arcB ornithine carbamoyltransferase HP15_3987 HP15_750
arcC carbamate kinase HP15_3988
odc L-ornithine decarboxylase HP15_3785
puuA glutamate-putrescine ligase HP15_942 HP15_428
puuB gamma-glutamylputrescine oxidase HP15_944
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase HP15_943 HP15_3144
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase HP15_2338
gabT gamma-aminobutyrate transaminase HP15_3708 HP15_2925
gabD succinate semialdehyde dehydrogenase HP15_3404 HP15_2020
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) HP15_3041 HP15_3040
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) HP15_3040 HP15_3041
astC succinylornithine transaminase HP15_3042 HP15_3708
astD succinylglutamate semialdehyde dehydrogenase HP15_3039 HP15_3945
astE succinylglutamate desuccinylase HP15_3034
atoB acetyl-CoA C-acetyltransferase HP15_2996 HP15_5
citrullinase putative citrullinase HP15_2074
davD glutarate semialdehyde dehydrogenase HP15_2020 HP15_3404
davT 5-aminovalerate aminotransferase HP15_3708 HP15_3042
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HP15_908 HP15_12
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HP15_1512 HP15_3941
gcdG succinyl-CoA:glutarate CoA-transferase HP15_1416 HP15_2609
gcdH glutaryl-CoA dehydrogenase HP15_3936 HP15_2
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) HP15_2488
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) HP15_2925 HP15_3042
patD gamma-aminobutyraldehyde dehydrogenase HP15_943 HP15_3626
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 HP15_287
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component HP15_3031
PS417_17595 ABC transporter for L-Citrulline, permease component 1 HP15_3032 HP15_3033
PS417_17600 ABC transporter for L-Citrulline, permease component 2 HP15_3033
PS417_17605 ABC transporter for L-Citrulline, ATPase component HP15_3030 HP15_2920
puo putrescine oxidase
put1 proline dehydrogenase HP15_2688
putA L-glutamate 5-semialdeyde dehydrogenase HP15_2688 HP15_3626
rocA 1-pyrroline-5-carboxylate dehydrogenase HP15_2688 HP15_3626
rocD ornithine aminotransferase HP15_3708 HP15_3855

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.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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