GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Bacteroides clarus YIT 12056

Best path

PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, rocA

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
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 BUB52_RS04930 BUB52_RS11690
citrullinase putative citrullinase BUB52_RS08840
rocD ornithine aminotransferase BUB52_RS04845 BUB52_RS13360
rocA 1-pyrroline-5-carboxylate dehydrogenase
Alternative steps:
AO353_03040 ABC transporter for L-Citrulline, ATPase component BUB52_RS11690 BUB52_RS14520
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03050 ABC transporter for L-Citrulline, permease component 1
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component
arcB ornithine carbamoyltransferase BUB52_RS13490
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase BUB52_RS13360 BUB52_RS04845
astD succinylglutamate semialdehyde dehydrogenase
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase
davD glutarate semialdehyde dehydrogenase
davT 5-aminovalerate aminotransferase BUB52_RS13360 BUB52_RS04845
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BUB52_RS00055
gabD succinate semialdehyde dehydrogenase
gabT gamma-aminobutyrate transaminase BUB52_RS13360 BUB52_RS04845
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
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) BUB52_RS13360 BUB52_RS04845
patD gamma-aminobutyraldehyde dehydrogenase
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC BUB52_RS08250
prdF proline racemase
PRO3 pyrroline-5-carboxylate reductase BUB52_RS13365
puo putrescine oxidase
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase
puuA glutamate-putrescine ligase BUB52_RS07230
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase

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