GapMind for catabolism of small carbon sources


L-citrulline catabolism in Pseudomonas fluorescens FW300-N2C3

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE

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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component AO356_18700 AO356_01470
AO353_03050 ABC transporter for L-Citrulline, permease component 1 AO356_18705 AO356_27115
AO353_03045 ABC transporter for L-Citrulline, permease component 2 AO356_18710 AO356_09910
AO353_03040 ABC transporter for L-Citrulline, ATPase component AO356_18715 AO356_05515
arcB ornithine carbamoyltransferase AO356_05275 AO356_18275
arcC carbamate kinase AO356_05280
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) AO356_18730 AO356_01525
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) AO356_18735 AO356_01530
astC succinylornithine transaminase AO356_18725 AO356_17010
astD succinylglutamate semialdehyde dehydrogenase AO356_18740 AO356_27965
astE succinylglutamate desuccinylase AO356_18755
Alternative steps:
atoB acetyl-CoA C-acetyltransferase AO356_21640 AO356_26350
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase AO356_10720 AO356_29070
davT 5-aminovalerate aminotransferase AO356_10715 AO356_26715
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AO356_26360 AO356_02330
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AO356_02330 AO356_29995
gabD succinate semialdehyde dehydrogenase AO356_10720 AO356_30285
gabT gamma-aminobutyrate transaminase AO356_13150 AO356_26715
gcdG succinyl-CoA:glutarate CoA-transferase AO356_10845 AO356_06355
gcdH glutaryl-CoA dehydrogenase AO356_10850 AO356_01580
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) AO356_26445
ocd ornithine cyclodeaminase AO356_29450
odc L-ornithine decarboxylase AO356_07310
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) AO356_13150 AO356_28705
patD gamma-aminobutyraldehyde dehydrogenase AO356_06315 AO356_06290
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase AO356_09240 AO356_24960
PRO3 pyrroline-5-carboxylate reductase AO356_13420 AO356_00600
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component AO356_05495 AO356_27120
PS417_17595 ABC transporter for L-Citrulline, permease component 1 AO356_27115 AO356_05500
PS417_17600 ABC transporter for L-Citrulline, permease component 2 AO356_27110 AO356_05505
PS417_17605 ABC transporter for L-Citrulline, ATPase component AO356_05515 AO356_27105
puo putrescine oxidase
put1 proline dehydrogenase AO356_09015
putA L-glutamate 5-semialdeyde dehydrogenase AO356_09015 AO356_07180
puuA glutamate-putrescine ligase AO356_13135 AO356_13145
puuB gamma-glutamylputrescine oxidase AO356_21495 AO356_12605
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AO356_12580 AO356_09270
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase AO356_13140
rocA 1-pyrroline-5-carboxylate dehydrogenase AO356_09015 AO356_07180
rocD ornithine aminotransferase AO356_17010 AO356_26715

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.



Related tools

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