GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Hippea alviniae EP5-r

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component
AO353_03050 ABC transporter for L-Citrulline, permease component 1 G415_RS0100535
AO353_03045 ABC transporter for L-Citrulline, permease component 2 G415_RS0100535
AO353_03040 ABC transporter for L-Citrulline, ATPase component G415_RS0100540 G415_RS0103225
arcB ornithine carbamoyltransferase G415_RS0107525 G415_RS0104265
arcC carbamate kinase
rocD ornithine aminotransferase G415_RS0106790
PRO3 pyrroline-5-carboxylate reductase G415_RS0103995
put1 proline dehydrogenase G415_RS0108290
putA L-glutamate 5-semialdeyde dehydrogenase G415_RS0108295 G415_RS0101870
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase G415_RS0106790 G415_RS0101830
astD succinylglutamate semialdehyde dehydrogenase G415_RS0101870
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase G415_RS0109095
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase G415_RS0101870
davT 5-aminovalerate aminotransferase G415_RS0106790 G415_RS0101830
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase G415_RS0105565 G415_RS0104835
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase G415_RS0100670
gabD succinate semialdehyde dehydrogenase G415_RS0101870
gabT gamma-aminobutyrate transaminase G415_RS0101830 G415_RS0106790
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase G415_RS0100700
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) G415_RS0106790
patD gamma-aminobutyraldehyde dehydrogenase G415_RS0101870
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
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 G415_RS0100540 G415_RS0103075
puo putrescine oxidase
puuA glutamate-putrescine ligase G415_RS0104980
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase G415_RS0101870
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase G415_RS0108295 G415_RS0101870

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 Apr 09 2024. 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