GapMind for catabolism of small carbon sources


L-citrulline catabolism in Shewanella sp. ANA-3

Best path

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

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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component
AO353_03050 ABC transporter for L-Citrulline, permease component 1 Shewana3_0881
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component Shewana3_0880 Shewana3_1538
arcB ornithine carbamoyltransferase Shewana3_3903 Shewana3_3070
arcC carbamate kinase
odc L-ornithine decarboxylase Shewana3_3871 Shewana3_3682
puuA glutamate-putrescine ligase Shewana3_3098 Shewana3_0300
puuB gamma-glutamylputrescine oxidase Shewana3_3093 Shewana3_3101
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Shewana3_3105 Shewana3_0250
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Shewana3_3099
gabT gamma-aminobutyrate transaminase Shewana3_3091 Shewana3_3106
gabD succinate semialdehyde dehydrogenase Shewana3_3092 Shewana3_3105
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) Shewana3_0611
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) Shewana3_0611
astC succinylornithine transaminase Shewana3_0610 Shewana3_3091
astD succinylglutamate semialdehyde dehydrogenase Shewana3_0612 Shewana3_0250
astE succinylglutamate desuccinylase Shewana3_2132
atoB acetyl-CoA C-acetyltransferase Shewana3_2771 Shewana3_0023
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase Shewana3_3092 Shewana3_3105
davT 5-aminovalerate aminotransferase Shewana3_3091 Shewana3_0610
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Shewana3_2768 Shewana3_0024
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Shewana3_0024 Shewana3_1461
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase Shewana3_1672 Shewana3_2769
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) Shewana3_3106 Shewana3_0610
patD gamma-aminobutyraldehyde dehydrogenase Shewana3_3105 Shewana3_0250
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 Shewana3_1193
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1 Shewana3_0881
PS417_17600 ABC transporter for L-Citrulline, permease component 2
PS417_17605 ABC transporter for L-Citrulline, ATPase component Shewana3_0880 Shewana3_3192
puo putrescine oxidase
put1 proline dehydrogenase Shewana3_0819
putA L-glutamate 5-semialdeyde dehydrogenase Shewana3_0819 Shewana3_0250
rocA 1-pyrroline-5-carboxylate dehydrogenase Shewana3_0819 Shewana3_0250
rocD ornithine aminotransferase Shewana3_3091 Shewana3_2520

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