GapMind for catabolism of small carbon sources


L-citrulline catabolism in Klebsiella michiganensis M5al

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 (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 BWI76_RS20340 BWI76_RS19240
AO353_03050 ABC transporter for L-Citrulline, permease component 1 BWI76_RS20330 BWI76_RS19235
AO353_03045 ABC transporter for L-Citrulline, permease component 2 BWI76_RS20325 BWI76_RS19230
AO353_03040 ABC transporter for L-Citrulline, ATPase component BWI76_RS20320 BWI76_RS07590
arcB ornithine carbamoyltransferase BWI76_RS03010 BWI76_RS17500
arcC carbamate kinase BWI76_RS07060 BWI76_RS17520
odc L-ornithine decarboxylase BWI76_RS24175 BWI76_RS07195
puuA glutamate-putrescine ligase BWI76_RS10710 BWI76_RS00400
puuB gamma-glutamylputrescine oxidase BWI76_RS10690
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BWI76_RS10695 BWI76_RS03865
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase BWI76_RS10705
gabT gamma-aminobutyrate transaminase BWI76_RS26375 BWI76_RS14455
gabD succinate semialdehyde dehydrogenase BWI76_RS05620 BWI76_RS10695
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) BWI76_RS11675
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) BWI76_RS11675
astC succinylornithine transaminase BWI76_RS11670 BWI76_RS26000
astD succinylglutamate semialdehyde dehydrogenase BWI76_RS11680 BWI76_RS13425
astE succinylglutamate desuccinylase BWI76_RS11690
atoB acetyl-CoA C-acetyltransferase BWI76_RS23445 BWI76_RS01360
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase BWI76_RS05620 BWI76_RS03865
davT 5-aminovalerate aminotransferase BWI76_RS26375 BWI76_RS14020
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BWI76_RS13115 BWI76_RS20455
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BWI76_RS01365 BWI76_RS20455
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
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) BWI76_RS24630 BWI76_RS14455
patD gamma-aminobutyraldehyde dehydrogenase BWI76_RS13425 BWI76_RS10695
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 BWI76_RS06170 BWI76_RS14970
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component BWI76_RS07345 BWI76_RS20340
PS417_17595 ABC transporter for L-Citrulline, permease component 1 BWI76_RS20330 BWI76_RS19235
PS417_17600 ABC transporter for L-Citrulline, permease component 2 BWI76_RS20325 BWI76_RS19230
PS417_17605 ABC transporter for L-Citrulline, ATPase component BWI76_RS20320 BWI76_RS10585
puo putrescine oxidase BWI76_RS13080
put1 proline dehydrogenase BWI76_RS10795
putA L-glutamate 5-semialdeyde dehydrogenase BWI76_RS10795 BWI76_RS07615
rocA 1-pyrroline-5-carboxylate dehydrogenase BWI76_RS10795 BWI76_RS07615
rocD ornithine aminotransferase BWI76_RS26375 BWI76_RS14020

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