GapMind for catabolism of small carbon sources


L-citrulline catabolism in Marinomonas arctica 328

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, aruF, aruG, astC, astD, astE


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 (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 DK187_RS13620
AO353_03050 ABC transporter for L-Citrulline, permease component 1 DK187_RS13625 DK187_RS16320
AO353_03045 ABC transporter for L-Citrulline, permease component 2 DK187_RS13630 DK187_RS16320
AO353_03040 ABC transporter for L-Citrulline, ATPase component DK187_RS13615 DK187_RS20495
citrullinase putative citrullinase DK187_RS07055
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) DK187_RS07640 DK187_RS07635
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) DK187_RS07635 DK187_RS07640
astC succinylornithine transaminase DK187_RS13600 DK187_RS13845
astD succinylglutamate semialdehyde dehydrogenase DK187_RS07630 DK187_RS02405
astE succinylglutamate desuccinylase DK187_RS13660
Alternative steps:
arcB ornithine carbamoyltransferase DK187_RS00395 DK187_RS15935
arcC carbamate kinase
atoB acetyl-CoA C-acetyltransferase DK187_RS06190 DK187_RS08790
davD glutarate semialdehyde dehydrogenase DK187_RS02405 DK187_RS15780
davT 5-aminovalerate aminotransferase DK187_RS02410 DK187_RS13600
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase DK187_RS04965 DK187_RS08785
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase DK187_RS08785 DK187_RS04955
gabD succinate semialdehyde dehydrogenase DK187_RS02405 DK187_RS18540
gabT gamma-aminobutyrate transaminase DK187_RS02410 DK187_RS08575
gcdG succinyl-CoA:glutarate CoA-transferase DK187_RS07920
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) DK187_RS04730
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase DK187_RS12845
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) DK187_RS08575 DK187_RS13600
patD gamma-aminobutyraldehyde dehydrogenase DK187_RS01055 DK187_RS17920
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase DK187_RS02370
PRO3 pyrroline-5-carboxylate reductase DK187_RS15955
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component DK187_RS13620
PS417_17595 ABC transporter for L-Citrulline, permease component 1 DK187_RS13625 DK187_RS13630
PS417_17600 ABC transporter for L-Citrulline, permease component 2 DK187_RS13630 DK187_RS16320
PS417_17605 ABC transporter for L-Citrulline, ATPase component DK187_RS13615 DK187_RS20495
puo putrescine oxidase
put1 proline dehydrogenase DK187_RS02925
putA L-glutamate 5-semialdeyde dehydrogenase DK187_RS02925 DK187_RS15725
puuA glutamate-putrescine ligase DK187_RS01010 DK187_RS01045
puuB gamma-glutamylputrescine oxidase DK187_RS01050 DK187_RS01015
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase DK187_RS01055 DK187_RS00035
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase DK187_RS02925 DK187_RS15725
rocD ornithine aminotransferase DK187_RS02410 DK187_RS13985

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