GapMind for catabolism of small carbon sources


L-citrulline catabolism in Aquimarina macrocephali JAMB N27

Best path

PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, PRO3, put1, putA


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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1
PS417_17600 ABC transporter for L-Citrulline, permease component 2
PS417_17605 ABC transporter for L-Citrulline, ATPase component Z054_RS0118835 Z054_RS0100810
citrullinase putative citrullinase Z054_RS0114895
rocD ornithine aminotransferase Z054_RS0124165 Z054_RS0116790
PRO3 pyrroline-5-carboxylate reductase Z054_RS0117460
put1 proline dehydrogenase Z054_RS0106545
putA L-glutamate 5-semialdeyde dehydrogenase Z054_RS0125405 Z054_RS0121915
Alternative steps:
AO353_03040 ABC transporter for L-Citrulline, ATPase component Z054_RS0118835 Z054_RS0108435
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03050 ABC transporter for L-Citrulline, permease component 1
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component
arcB ornithine carbamoyltransferase Z054_RS0106805 Z054_RS0117470
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase Z054_RS0124165 Z054_RS0117465
astD succinylglutamate semialdehyde dehydrogenase Z054_RS0105015 Z054_RS0121915
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Z054_RS0106210 Z054_RS0115825
davD glutarate semialdehyde dehydrogenase Z054_RS0121915 Z054_RS0121900
davT 5-aminovalerate aminotransferase Z054_RS0124165 Z054_RS0107025
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Z054_RS0106865 Z054_RS0108580
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Z054_RS0115830 Z054_RS0112885
gabD succinate semialdehyde dehydrogenase Z054_RS0121900 Z054_RS0121915
gabT gamma-aminobutyrate transaminase Z054_RS0124165 Z054_RS0107025
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase Z054_RS0123520 Z054_RS0121070
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) Z054_RS0117465 Z054_RS0116790
patD gamma-aminobutyraldehyde dehydrogenase Z054_RS0121900 Z054_RS0110935
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Z054_RS0123730 Z054_RS0121525
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Z054_RS0121900 Z054_RS0110935
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase Z054_RS0125405 Z054_RS0121915

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