GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Pseudomonas baetica a390

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component C0J26_RS10590 C0J26_RS16195
AO353_03050 ABC transporter for L-Citrulline, permease component 1 C0J26_RS10595 C0J26_RS08825
AO353_03045 ABC transporter for L-Citrulline, permease component 2 C0J26_RS10600 C0J26_RS01680
AO353_03040 ABC transporter for L-Citrulline, ATPase component C0J26_RS10610 C0J26_RS08810
arcB ornithine carbamoyltransferase C0J26_RS20830 C0J26_RS21570
arcC carbamate kinase C0J26_RS20835
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) C0J26_RS10635 C0J26_RS16245
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) C0J26_RS10640 C0J26_RS16250
astC succinylornithine transaminase C0J26_RS10630 C0J26_RS22150
astD succinylglutamate semialdehyde dehydrogenase C0J26_RS10645 C0J26_RS15895
astE succinylglutamate desuccinylase C0J26_RS10660
Alternative steps:
atoB acetyl-CoA C-acetyltransferase C0J26_RS15230 C0J26_RS16155
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase C0J26_RS01025 C0J26_RS12950
davT 5-aminovalerate aminotransferase C0J26_RS01030 C0J26_RS25540
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase C0J26_RS15240 C0J26_RS25285
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase C0J26_RS25285 C0J26_RS22935
gabD succinate semialdehyde dehydrogenase C0J26_RS01025 C0J26_RS12640
gabT gamma-aminobutyrate transaminase C0J26_RS29440 C0J26_RS01030
gcdG succinyl-CoA:glutarate CoA-transferase C0J26_RS00750 C0J26_RS06235
gcdH glutaryl-CoA dehydrogenase C0J26_RS00745 C0J26_RS16985
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 C0J26_RS04915 C0J26_RS12010
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) C0J26_RS29440 C0J26_RS04130
patD gamma-aminobutyraldehyde dehydrogenase C0J26_RS30270 C0J26_RS15895
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 C0J26_RS29000
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component C0J26_RS08830 C0J26_RS10590
PS417_17595 ABC transporter for L-Citrulline, permease component 1 C0J26_RS08825 C0J26_RS10595
PS417_17600 ABC transporter for L-Citrulline, permease component 2 C0J26_RS08820 C0J26_RS10600
PS417_17605 ABC transporter for L-Citrulline, ATPase component C0J26_RS08810 C0J26_RS10610
puo putrescine oxidase
put1 proline dehydrogenase C0J26_RS02535
putA L-glutamate 5-semialdeyde dehydrogenase C0J26_RS02535 C0J26_RS05085
puuA glutamate-putrescine ligase C0J26_RS29450 C0J26_RS15900
puuB gamma-glutamylputrescine oxidase C0J26_RS18685 C0J26_RS15890
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase C0J26_RS30270 C0J26_RS15895
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase C0J26_RS15905
rocA 1-pyrroline-5-carboxylate dehydrogenase C0J26_RS02535 C0J26_RS05085
rocD ornithine aminotransferase C0J26_RS22150 C0J26_RS01030

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