GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Rhodobacter viridis JA737

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component C8J30_RS16135 C8J30_RS12900
AO353_03050 ABC transporter for L-Citrulline, permease component 1 C8J30_RS16140 C8J30_RS16145
AO353_03045 ABC transporter for L-Citrulline, permease component 2 C8J30_RS16145 C8J30_RS12910
AO353_03040 ABC transporter for L-Citrulline, ATPase component C8J30_RS16150 C8J30_RS12895
arcB ornithine carbamoyltransferase C8J30_RS11910 C8J30_RS06260
arcC carbamate kinase
odc L-ornithine decarboxylase C8J30_RS06735
puuA glutamate-putrescine ligase C8J30_RS12930 C8J30_RS06155
puuB gamma-glutamylputrescine oxidase C8J30_RS12935 C8J30_RS13680
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase C8J30_RS10160 C8J30_RS14450
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase C8J30_RS00720 C8J30_RS00440
gabT gamma-aminobutyrate transaminase C8J30_RS12000 C8J30_RS09725
gabD succinate semialdehyde dehydrogenase C8J30_RS06315 C8J30_RS10160
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase C8J30_RS11905 C8J30_RS12000
astD succinylglutamate semialdehyde dehydrogenase C8J30_RS15880 C8J30_RS16955
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase C8J30_RS12155 C8J30_RS14960
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase C8J30_RS06315 C8J30_RS08590
davT 5-aminovalerate aminotransferase C8J30_RS12000 C8J30_RS00085
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase C8J30_RS04555 C8J30_RS06890
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase C8J30_RS06890 C8J30_RS05595
gcdG succinyl-CoA:glutarate CoA-transferase C8J30_RS10955
gcdH glutaryl-CoA dehydrogenase C8J30_RS04420 C8J30_RS00780
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
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) C8J30_RS09725 C8J30_RS00085
patD gamma-aminobutyraldehyde dehydrogenase C8J30_RS08590 C8J30_RS10160
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 C8J30_RS11325
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component C8J30_RS16135
PS417_17595 ABC transporter for L-Citrulline, permease component 1 C8J30_RS16140 C8J30_RS06530
PS417_17600 ABC transporter for L-Citrulline, permease component 2 C8J30_RS12910 C8J30_RS16145
PS417_17605 ABC transporter for L-Citrulline, ATPase component C8J30_RS16150 C8J30_RS12895
puo putrescine oxidase
put1 proline dehydrogenase C8J30_RS10945
putA L-glutamate 5-semialdeyde dehydrogenase C8J30_RS10945 C8J30_RS15880
rocA 1-pyrroline-5-carboxylate dehydrogenase C8J30_RS10945 C8J30_RS15880
rocD ornithine aminotransferase C8J30_RS12000 C8J30_RS00315

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