GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Malonomonas rubra DSM 5091

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 (27 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 BUB13_RS12685
AO353_03045 ABC transporter for L-Citrulline, permease component 2 BUB13_RS12685 BUB13_RS17605
AO353_03040 ABC transporter for L-Citrulline, ATPase component BUB13_RS11695 BUB13_RS17610
arcB ornithine carbamoyltransferase BUB13_RS15125 BUB13_RS17580
arcC carbamate kinase BUB13_RS15350
rocD ornithine aminotransferase BUB13_RS15120 BUB13_RS11855
PRO3 pyrroline-5-carboxylate reductase BUB13_RS11555
put1 proline dehydrogenase BUB13_RS10010
putA L-glutamate 5-semialdeyde dehydrogenase BUB13_RS10015
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase BUB13_RS15120 BUB13_RS11855
astD succinylglutamate semialdehyde dehydrogenase
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase
citrullinase putative citrullinase BUB13_RS04170
davD glutarate semialdehyde dehydrogenase
davT 5-aminovalerate aminotransferase BUB13_RS15120 BUB13_RS08945
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BUB13_RS00930 BUB13_RS05985
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BUB13_RS03185
gabD succinate semialdehyde dehydrogenase BUB13_RS11870 BUB13_RS03800
gabT gamma-aminobutyrate transaminase BUB13_RS15120 BUB13_RS11855
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) BUB13_RS04425
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase BUB13_RS04490
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 BUB13_RS17685
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) BUB13_RS15120 BUB13_RS11855
patD gamma-aminobutyraldehyde dehydrogenase
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC BUB13_RS17105
prdF proline racemase
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1 BUB13_RS12685 BUB13_RS17605
PS417_17600 ABC transporter for L-Citrulline, permease component 2 BUB13_RS17605
PS417_17605 ABC transporter for L-Citrulline, ATPase component BUB13_RS11695 BUB13_RS17610
puo putrescine oxidase
puuA glutamate-putrescine ligase BUB13_RS00250
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase BUB13_RS06250
rocA 1-pyrroline-5-carboxylate dehydrogenase BUB13_RS10015

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