GapMind for catabolism of small carbon sources


L-citrulline catabolism in Pseudomonas simiae WCS417

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE

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 PS417_21745 PS417_10900
AO353_03050 ABC transporter for L-Citrulline, permease component 1 PS417_21740 PS417_17595
AO353_03045 ABC transporter for L-Citrulline, permease component 2 PS417_21735 PS417_01485
AO353_03040 ABC transporter for L-Citrulline, ATPase component PS417_21725 PS417_06395
arcB ornithine carbamoyltransferase PS417_22335 PS417_05595
arcC carbamate kinase PS417_22340
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) PS417_21705 PS417_21700
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) PS417_21700 PS417_21705
astC succinylornithine transaminase PS417_21710 PS417_08025
astD succinylglutamate semialdehyde dehydrogenase PS417_21695 PS417_04200
astE succinylglutamate desuccinylase PS417_21680
Alternative steps:
atoB acetyl-CoA C-acetyltransferase PS417_10515 PS417_13855
citrullinase putative citrullinase PS417_17580
davD glutarate semialdehyde dehydrogenase PS417_00895 PS417_17840
davT 5-aminovalerate aminotransferase PS417_00900 PS417_23355
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PS417_13845 PS417_07575
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PS417_07575 PS417_21215
gabD succinate semialdehyde dehydrogenase PS417_00895 PS417_18705
gabT gamma-aminobutyrate transaminase PS417_27130 PS417_00900
gcdG succinyl-CoA:glutarate CoA-transferase PS417_00585 PS417_14920
gcdH glutaryl-CoA dehydrogenase PS417_00580 PS417_17015
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase PS417_17585
odc L-ornithine decarboxylase PS417_04005 PS417_12240
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) PS417_27130 PS417_11165
patD gamma-aminobutyraldehyde dehydrogenase PS417_05920 PS417_05945
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase PS417_14305
PRO3 pyrroline-5-carboxylate reductase PS417_26730
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component PS417_17590 PS417_06415
PS417_17595 ABC transporter for L-Citrulline, permease component 1 PS417_17595 PS417_06410
PS417_17600 ABC transporter for L-Citrulline, permease component 2 PS417_17600 PS417_06405
PS417_17605 ABC transporter for L-Citrulline, ATPase component PS417_17605 PS417_06395
puo putrescine oxidase
put1 proline dehydrogenase PS417_02175
putA L-glutamate 5-semialdeyde dehydrogenase PS417_02175 PS417_04200
puuA glutamate-putrescine ligase PS417_27140 PS417_27135
puuB gamma-glutamylputrescine oxidase PS417_18505 PS417_27720
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PS417_27745 PS417_26340
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase PS417_02175 PS417_04200
rocD ornithine aminotransferase PS417_08025 PS417_00900

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