GapMind for catabolism of small carbon sources


L-citrulline catabolism in Azospirillum brasilense Sp245

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, 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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component AZOBR_RS27130 AZOBR_RS00685
AO353_03050 ABC transporter for L-Citrulline, permease component 1 AZOBR_RS00680 AZOBR_RS23520
AO353_03045 ABC transporter for L-Citrulline, permease component 2 AZOBR_RS00675 AZOBR_RS18070
AO353_03040 ABC transporter for L-Citrulline, ATPase component AZOBR_RS00690 AZOBR_RS23525
arcB ornithine carbamoyltransferase AZOBR_RS13250 AZOBR_RS19030
arcC carbamate kinase AZOBR_RS13245
rocD ornithine aminotransferase AZOBR_RS19590 AZOBR_RS19630
PRO3 pyrroline-5-carboxylate reductase AZOBR_RS06245
put1 proline dehydrogenase AZOBR_RS23695
putA L-glutamate 5-semialdeyde dehydrogenase AZOBR_RS23695 AZOBR_RS29185
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase AZOBR_RS19025 AZOBR_RS19590
astD succinylglutamate semialdehyde dehydrogenase AZOBR_RS09720 AZOBR_RS19635
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase AZOBR_RS30610 AZOBR_RS28180
citrullinase putative citrullinase AZOBR_RS08170
davD glutarate semialdehyde dehydrogenase AZOBR_RS09720 AZOBR_RS19635
davT 5-aminovalerate aminotransferase AZOBR_RS19630 AZOBR_RS19025
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AZOBR_RS01260 AZOBR_RS26485
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AZOBR_RS20225 AZOBR_RS29225
gabD succinate semialdehyde dehydrogenase AZOBR_RS09720 AZOBR_RS19635
gabT gamma-aminobutyrate transaminase AZOBR_RS19630 AZOBR_RS03635
gcdG succinyl-CoA:glutarate CoA-transferase AZOBR_RS19675 AZOBR_RS29180
gcdH glutaryl-CoA dehydrogenase AZOBR_RS19670 AZOBR_RS22310
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) AZOBR_RS33525
ocd ornithine cyclodeaminase AZOBR_RS03120
odc L-ornithine decarboxylase AZOBR_RS27535 AZOBR_RS00105
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) AZOBR_RS03635 AZOBR_RS22505
patD gamma-aminobutyraldehyde dehydrogenase AZOBR_RS22315 AZOBR_RS19635
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase AZOBR_RS27830
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component AZOBR_RS27130
PS417_17595 ABC transporter for L-Citrulline, permease component 1 AZOBR_RS00680 AZOBR_RS23520
PS417_17600 ABC transporter for L-Citrulline, permease component 2 AZOBR_RS00675 AZOBR_RS00680
PS417_17605 ABC transporter for L-Citrulline, ATPase component AZOBR_RS00690 AZOBR_RS26405
puo putrescine oxidase
puuA glutamate-putrescine ligase AZOBR_RS08850
puuB gamma-glutamylputrescine oxidase AZOBR_RS08855 AZOBR_RS25655
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AZOBR_RS09720 AZOBR_RS19635
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase AZOBR_RS02010 AZOBR_RS00395
rocA 1-pyrroline-5-carboxylate dehydrogenase AZOBR_RS23695 AZOBR_RS29185

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