GapMind for catabolism of small carbon sources


L-citrulline catabolism in Desulfovibrio vulgaris Miyazaki F

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA

Also see fitness data for the top candidates


Overview: Citrulline can be catabolized via ornithine carbamoyltransferase in reverse (PMID:3129535). Genetic evidence suggests that some bacteria use a putative citrullinase (EC 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 DvMF_0860 DvMF_1571
AO353_03050 ABC transporter for L-Citrulline, permease component 1 DvMF_1570 DvMF_1568
AO353_03045 ABC transporter for L-Citrulline, permease component 2 DvMF_1568 DvMF_0861
AO353_03040 ABC transporter for L-Citrulline, ATPase component DvMF_1920 DvMF_1342
citrullinase putative citrullinase DvMF_0653
rocD ornithine aminotransferase DvMF_0516 DvMF_2502
PRO3 pyrroline-5-carboxylate reductase DvMF_3161
put1 proline dehydrogenase DvMF_2146
putA L-glutamate 5-semialdeyde dehydrogenase DvMF_2146
Alternative steps:
arcB ornithine carbamoyltransferase DvMF_0046 DvMF_1425
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase DvMF_3149 DvMF_0516
astD succinylglutamate semialdehyde dehydrogenase DvMF_2146
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase
davD glutarate semialdehyde dehydrogenase DvMF_2146
davT 5-aminovalerate aminotransferase DvMF_1002 DvMF_3149
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase
gabD succinate semialdehyde dehydrogenase DvMF_2322 DvMF_2146
gabT gamma-aminobutyrate transaminase DvMF_0516 DvMF_1002
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) DvMF_0516 DvMF_3149
patD gamma-aminobutyraldehyde dehydrogenase DvMF_2146
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
PS417_17595 ABC transporter for L-Citrulline, permease component 1 DvMF_1570 DvMF_1919
PS417_17600 ABC transporter for L-Citrulline, permease component 2 DvMF_3154 DvMF_1568
PS417_17605 ABC transporter for L-Citrulline, ATPase component DvMF_1920 DvMF_2788
puo putrescine oxidase
puuA glutamate-putrescine ligase DvMF_2099
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase DvMF_2146
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase DvMF_0015
rocA 1-pyrroline-5-carboxylate dehydrogenase DvMF_2146

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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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