GapMind for catabolism of small carbon sources


L-citrulline catabolism in Ruegeria conchae TW15

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, 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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component G7G_RS0105145
AO353_03050 ABC transporter for L-Citrulline, permease component 1 G7G_RS0111530 G7G_RS0105140
AO353_03045 ABC transporter for L-Citrulline, permease component 2 G7G_RS0111530 G7G_RS0105135
AO353_03040 ABC transporter for L-Citrulline, ATPase component G7G_RS0105150 G7G_RS0111050
citrullinase putative citrullinase G7G_RS0105980
ocd ornithine cyclodeaminase G7G_RS0105975
put1 proline dehydrogenase G7G_RS0112935
putA L-glutamate 5-semialdeyde dehydrogenase G7G_RS0112935 G7G_RS0110305
Alternative steps:
arcB ornithine carbamoyltransferase G7G_RS0112220 G7G_RS0121870
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase G7G_RS0112215 G7G_RS0106455
astD succinylglutamate semialdehyde dehydrogenase G7G_RS0110075 G7G_RS0121155
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase G7G_RS0122070 G7G_RS0116445
davD glutarate semialdehyde dehydrogenase G7G_RS0118970 G7G_RS0122450
davT 5-aminovalerate aminotransferase G7G_RS0121165 G7G_RS0112215
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase G7G_RS0116465 G7G_RS0104515
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase G7G_RS0102205 G7G_RS0108810
gabD succinate semialdehyde dehydrogenase G7G_RS0118970 G7G_RS0110305
gabT gamma-aminobutyrate transaminase G7G_RS0101175 G7G_RS0109195
gcdG succinyl-CoA:glutarate CoA-transferase G7G_RS0104670 G7G_RS0122435
gcdH glutaryl-CoA dehydrogenase G7G_RS0107335 G7G_RS0117695
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
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 G7G_RS0115185
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) G7G_RS0109195 G7G_RS0101175
patD gamma-aminobutyraldehyde dehydrogenase G7G_RS0103600 G7G_RS0121155
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase G7G_RS0111270 G7G_RS0111830
PRO3 pyrroline-5-carboxylate reductase G7G_RS0112680
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1 G7G_RS0111055 G7G_RS0111530
PS417_17600 ABC transporter for L-Citrulline, permease component 2 G7G_RS0105135
PS417_17605 ABC transporter for L-Citrulline, ATPase component G7G_RS0105150 G7G_RS0101315
puo putrescine oxidase
puuA glutamate-putrescine ligase G7G_RS0105115 G7G_RS0105125
puuB gamma-glutamylputrescine oxidase G7G_RS0105110 G7G_RS0110025
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase G7G_RS0108790 G7G_RS0121155
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase G7G_RS0117835
rocA 1-pyrroline-5-carboxylate dehydrogenase G7G_RS0112935 G7G_RS0110305
rocD ornithine aminotransferase G7G_RS0121165 G7G_RS0121130

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