GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Gallaecimonas xiamenensis 3-C-1

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, aruF, aruG, astC, astD, astE

Rules

Overview: Citrulline can be catabolized via ornithine carbamoyltransferase in reverse (PMID:3129535). Genetic evidence suggests that some bacteria use a putative citrullinase (EC 3.5.1.20) to consume citrulline.

51 steps (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component B3C1_RS06770
AO353_03050 ABC transporter for L-Citrulline, permease component 1
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component B3C1_RS12960 B3C1_RS03530
citrullinase putative citrullinase B3C1_RS08705 B3C1_RS12980
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) B3C1_RS02880
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) B3C1_RS02880
astC succinylornithine transaminase B3C1_RS02875 B3C1_RS09655
astD succinylglutamate semialdehyde dehydrogenase B3C1_RS02885 B3C1_RS14130
astE succinylglutamate desuccinylase B3C1_RS00790
Alternative steps:
arcB ornithine carbamoyltransferase B3C1_RS02720 B3C1_RS09745
arcC carbamate kinase
atoB acetyl-CoA C-acetyltransferase B3C1_RS14955 B3C1_RS13505
davD glutarate semialdehyde dehydrogenase B3C1_RS02820 B3C1_RS03260
davT 5-aminovalerate aminotransferase B3C1_RS02875 B3C1_RS09655
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase B3C1_RS17620 B3C1_RS13490
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase B3C1_RS17620 B3C1_RS04935
gabD succinate semialdehyde dehydrogenase B3C1_RS02820 B3C1_RS08870
gabT gamma-aminobutyrate transaminase B3C1_RS02875 B3C1_RS11725
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase B3C1_RS13525 B3C1_RS13495
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) B3C1_RS12090
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) B3C1_RS12095
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) B3C1_RS02875 B3C1_RS09655
patD gamma-aminobutyraldehyde dehydrogenase B3C1_RS03260 B3C1_RS02820
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 B3C1_RS06465
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 B3C1_RS03280 B3C1_RS08485
puo putrescine oxidase
put1 proline dehydrogenase B3C1_RS14130
putA L-glutamate 5-semialdeyde dehydrogenase B3C1_RS14130 B3C1_RS02820
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase B3C1_RS03260 B3C1_RS02820
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase B3C1_RS14130 B3C1_RS02820
rocD ornithine aminotransferase B3C1_RS02875 B3C1_RS09655

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 24 2021. The underlying query database was built on Sep 17 2021.

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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