GapMind for catabolism of small carbon sources


L-citrulline catabolism in Dyella japonica UNC79MFTsu3.2

Best path

PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, PRO3, put1, putA

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
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 N515DRAFT_1085 N515DRAFT_2216
citrullinase putative citrullinase N515DRAFT_1536
rocD ornithine aminotransferase N515DRAFT_3630 N515DRAFT_3308
PRO3 pyrroline-5-carboxylate reductase N515DRAFT_1783
put1 proline dehydrogenase N515DRAFT_4232 N515DRAFT_0956
putA L-glutamate 5-semialdeyde dehydrogenase N515DRAFT_4232 N515DRAFT_3729
Alternative steps:
AO353_03040 ABC transporter for L-Citrulline, ATPase component N515DRAFT_1085 N515DRAFT_1562
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03050 ABC transporter for L-Citrulline, permease component 1
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component
arcB ornithine carbamoyltransferase N515DRAFT_3763 N515DRAFT_1776
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase N515DRAFT_3308 N515DRAFT_1751
astD succinylglutamate semialdehyde dehydrogenase N515DRAFT_3729 N515DRAFT_4232
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase N515DRAFT_0938 N515DRAFT_2688
davD glutarate semialdehyde dehydrogenase N515DRAFT_3729 N515DRAFT_2488
davT 5-aminovalerate aminotransferase N515DRAFT_3308 N515DRAFT_1751
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase N515DRAFT_1164 N515DRAFT_0416
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase N515DRAFT_2687 N515DRAFT_0416
gabD succinate semialdehyde dehydrogenase N515DRAFT_2488 N515DRAFT_3729
gabT gamma-aminobutyrate transaminase N515DRAFT_3308 N515DRAFT_1751
gcdG succinyl-CoA:glutarate CoA-transferase N515DRAFT_3223
gcdH glutaryl-CoA dehydrogenase N515DRAFT_0484 N515DRAFT_0492
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase
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) N515DRAFT_3308 N515DRAFT_1751
patD gamma-aminobutyraldehyde dehydrogenase N515DRAFT_3729 N515DRAFT_2488
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase N515DRAFT_0959
puo putrescine oxidase
puuA glutamate-putrescine ligase N515DRAFT_3024
puuB gamma-glutamylputrescine oxidase N515DRAFT_2697
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase N515DRAFT_3729 N515DRAFT_0379
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase N515DRAFT_4232 N515DRAFT_3729

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