GapMind for catabolism of small carbon sources


L-citrulline catabolism in Caulobacter crescentus NA1000

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, 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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component CCNA_01508
AO353_03050 ABC transporter for L-Citrulline, permease component 1 CCNA_01507
AO353_03045 ABC transporter for L-Citrulline, permease component 2 CCNA_01507
AO353_03040 ABC transporter for L-Citrulline, ATPase component CCNA_01506 CCNA_02751
citrullinase putative citrullinase CCNA_00212
odc L-ornithine decarboxylase CCNA_00365
puuA glutamate-putrescine ligase CCNA_03230 CCNA_03240
puuB gamma-glutamylputrescine oxidase CCNA_03229
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase CCNA_03243 CCNA_03695
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase CCNA_03234
gabT gamma-aminobutyrate transaminase CCNA_03233 CCNA_03245
gabD succinate semialdehyde dehydrogenase CCNA_03242 CCNA_03243
Alternative steps:
arcB ornithine carbamoyltransferase CCNA_02325 CCNA_02525
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) CCNA_01678 CCNA_00617
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) CCNA_00617 CCNA_01678
astC succinylornithine transaminase CCNA_00620 CCNA_02326
astD succinylglutamate semialdehyde dehydrogenase CCNA_01679 CCNA_00618
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase CCNA_00820 CCNA_00544
davD glutarate semialdehyde dehydrogenase CCNA_03242 CCNA_03243
davT 5-aminovalerate aminotransferase CCNA_00620 CCNA_02326
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CCNA_00006 CCNA_01794
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CCNA_00123 CCNA_03293
gcdG succinyl-CoA:glutarate CoA-transferase CCNA_03677 CCNA_02410
gcdH glutaryl-CoA dehydrogenase CCNA_02254 CCNA_01412
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) CCNA_03278
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) CCNA_03233 CCNA_03245
patD gamma-aminobutyraldehyde dehydrogenase CCNA_03243 CCNA_03695
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 CCNA_00528
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component CCNA_01508
PS417_17595 ABC transporter for L-Citrulline, permease component 1
PS417_17600 ABC transporter for L-Citrulline, permease component 2 CCNA_01507
PS417_17605 ABC transporter for L-Citrulline, ATPase component CCNA_01506 CCNA_02751
puo putrescine oxidase
put1 proline dehydrogenase CCNA_00846
putA L-glutamate 5-semialdeyde dehydrogenase CCNA_00846 CCNA_00865
rocA 1-pyrroline-5-carboxylate dehydrogenase CCNA_00846 CCNA_00865
rocD ornithine aminotransferase CCNA_03233 CCNA_02326

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:

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