GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Desulfovibrio vulgaris Hildenborough

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component DVU0386 DVU1238
AO353_03050 ABC transporter for L-Citrulline, permease component 1 DVU0387 DVU0674
AO353_03045 ABC transporter for L-Citrulline, permease component 2 DVU0389 DVU0967
AO353_03040 ABC transporter for L-Citrulline, ATPase component DVU0105 DVU2343
arcB ornithine carbamoyltransferase DVU1096 DVU2901
arcC carbamate kinase
rocD ornithine aminotransferase DVU2559 DVU3168
PRO3 pyrroline-5-carboxylate reductase DVU2332
put1 proline dehydrogenase DVU3319
putA L-glutamate 5-semialdeyde dehydrogenase DVU3319 DVU3294
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase DVU2347 DVU2559
astD succinylglutamate semialdehyde dehydrogenase DVU3319
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase DVU3294 DVU3319
davT 5-aminovalerate aminotransferase DVU2559 DVU2347
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase 206645
gabD succinate semialdehyde dehydrogenase DVU3294 DVU3319
gabT gamma-aminobutyrate transaminase DVU2559 DVU2347
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) DVU2559 DVU2347
patD gamma-aminobutyraldehyde dehydrogenase DVU3319 DVU3294
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 DVU1238
PS417_17595 ABC transporter for L-Citrulline, permease component 1 DVU1237 DVU0387
PS417_17600 ABC transporter for L-Citrulline, permease component 2 DVU2340 DVU0389
PS417_17605 ABC transporter for L-Citrulline, ATPase component DVU0105 DVU1236
puo putrescine oxidase
puuA glutamate-putrescine ligase DVU3392
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase DVU3319 DVU3294
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase DVU3319 DVU3294

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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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