GapMind for catabolism of small carbon sources


L-citrulline catabolism in Pseudomonas fluorescens FW300-N1B4

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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component Pf1N1B4_3431 Pf1N1B4_5844
AO353_03050 ABC transporter for L-Citrulline, permease component 1 Pf1N1B4_3432 Pf1N1B4_4399
AO353_03045 ABC transporter for L-Citrulline, permease component 2 Pf1N1B4_3433 Pf1N1B4_4398
AO353_03040 ABC transporter for L-Citrulline, ATPase component Pf1N1B4_3435 Pf1N1B4_4396
arcB ornithine carbamoyltransferase Pf1N1B4_616 Pf1N1B4_762
arcC carbamate kinase Pf1N1B4_617
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) Pf1N1B4_3442 Pf1N1B4_5856
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) Pf1N1B4_3443 Pf1N1B4_4797
astC succinylornithine transaminase Pf1N1B4_3440 Pf1N1B4_2980
astD succinylglutamate semialdehyde dehydrogenase Pf1N1B4_3444 Pf1N1B4_3024
astE succinylglutamate desuccinylase Pf1N1B4_3447
Alternative steps:
atoB acetyl-CoA C-acetyltransferase Pf1N1B4_4786 Pf1N1B4_5835
citrullinase putative citrullinase Pf1N1B4_4796 Pf1N1B4_1662
davD glutarate semialdehyde dehydrogenase Pf1N1B4_1734 Pf1N1B4_4931
davT 5-aminovalerate aminotransferase Pf1N1B4_1733 Pf1N1B4_4910
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf1N1B4_4788 Pf1N1B4_3903
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf1N1B4_3903 Pf1N1B4_5134
gabD succinate semialdehyde dehydrogenase Pf1N1B4_1734 Pf1N1B4_5616
gabT gamma-aminobutyrate transaminase Pf1N1B4_2257 Pf1N1B4_1733
gcdG succinyl-CoA:glutarate CoA-transferase Pf1N1B4_1815 Pf1N1B4_5611
gcdH glutaryl-CoA dehydrogenase Pf1N1B4_1816 Pf1N1B4_3987
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Pf1N1B4_4264
ocd ornithine cyclodeaminase Pf1N1B4_4977
odc L-ornithine decarboxylase Pf1N1B4_1136 Pf1N1B4_4600
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) Pf1N1B4_2257 Pf1N1B4_1239
patD gamma-aminobutyraldehyde dehydrogenase Pf1N1B4_3024 Pf1N1B4_3029
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Pf1N1B4_5964 Pf1N1B4_5975
PRO3 pyrroline-5-carboxylate reductase Pf1N1B4_2341
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component Pf1N1B4_4791 Pf1N1B4_3179
PS417_17595 ABC transporter for L-Citrulline, permease component 1 Pf1N1B4_4792 Pf1N1B4_3178
PS417_17600 ABC transporter for L-Citrulline, permease component 2 Pf1N1B4_3177 Pf1N1B4_4398
PS417_17605 ABC transporter for L-Citrulline, ATPase component Pf1N1B4_4794 Pf1N1B4_3175
puo putrescine oxidase
put1 proline dehydrogenase Pf1N1B4_1489
putA L-glutamate 5-semialdeyde dehydrogenase Pf1N1B4_1489 Pf1N1B4_1109
puuA glutamate-putrescine ligase Pf1N1B4_4354 Pf1N1B4_2254
puuB gamma-glutamylputrescine oxidase Pf1N1B4_6047 Pf1N1B4_4356
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Pf1N1B4_2132 Pf1N1B4_4355
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Pf1N1B4_4353 Pf1N1B4_2255
rocA 1-pyrroline-5-carboxylate dehydrogenase Pf1N1B4_1489 Pf1N1B4_1109
rocD ornithine aminotransferase Pf1N1B4_2980 Pf1N1B4_4910

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