GapMind for catabolism of small carbon sources


L-citrulline catabolism in Pseudomonas fluorescens GW456-L13

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component PfGW456L13_1964 PfGW456L13_3699
AO353_03050 ABC transporter for L-Citrulline, permease component 1 PfGW456L13_1965 PfGW456L13_3700
AO353_03045 ABC transporter for L-Citrulline, permease component 2 PfGW456L13_1966 PfGW456L13_3701
AO353_03040 ABC transporter for L-Citrulline, ATPase component PfGW456L13_1967 PfGW456L13_3703
arcB ornithine carbamoyltransferase PfGW456L13_1873 PfGW456L13_1739
arcC carbamate kinase PfGW456L13_1872
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) PfGW456L13_1972 PfGW456L13_1973
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) PfGW456L13_1973 PfGW456L13_1972
astC succinylornithine transaminase PfGW456L13_1971 PfGW456L13_4910
astD succinylglutamate semialdehyde dehydrogenase PfGW456L13_1974 PfGW456L13_3205
astE succinylglutamate desuccinylase PfGW456L13_1977
Alternative steps:
atoB acetyl-CoA C-acetyltransferase PfGW456L13_2411 PfGW456L13_2982
citrullinase putative citrullinase PfGW456L13_2704
davD glutarate semialdehyde dehydrogenase PfGW456L13_495 PfGW456L13_3737
davT 5-aminovalerate aminotransferase PfGW456L13_494 PfGW456L13_4982
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PfGW456L13_2984 PfGW456L13_2434
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PfGW456L13_4041 PfGW456L13_3873
gabD succinate semialdehyde dehydrogenase PfGW456L13_495 PfGW456L13_3880
gabT gamma-aminobutyrate transaminase PfGW456L13_927 PfGW456L13_1398
gcdG succinyl-CoA:glutarate CoA-transferase PfGW456L13_553 PfGW456L13_3635
gcdH glutaryl-CoA dehydrogenase PfGW456L13_554 PfGW456L13_2591
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 PfGW456L13_5067 PfGW456L13_3336
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) PfGW456L13_927 PfGW456L13_1398
patD gamma-aminobutyraldehyde dehydrogenase PfGW456L13_4766 PfGW456L13_4760
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase PfGW456L13_3147 PfGW456L13_3583
PRO3 pyrroline-5-carboxylate reductase PfGW456L13_1010
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component PfGW456L13_383 PfGW456L13_4635
PS417_17595 ABC transporter for L-Citrulline, permease component 1 PfGW456L13_384 PfGW456L13_4636
PS417_17600 ABC transporter for L-Citrulline, permease component 2 PfGW456L13_4637 PfGW456L13_385
PS417_17605 ABC transporter for L-Citrulline, ATPase component PfGW456L13_386 PfGW456L13_4639
puo putrescine oxidase PfGW456L13_2439
put1 proline dehydrogenase PfGW456L13_223
putA L-glutamate 5-semialdeyde dehydrogenase PfGW456L13_223 PfGW456L13_5044
puuA glutamate-putrescine ligase PfGW456L13_925 PfGW456L13_926
puuB gamma-glutamylputrescine oxidase PfGW456L13_3923 PfGW456L13_809
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PfGW456L13_805 PfGW456L13_1397
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase PfGW456L13_223 PfGW456L13_5044
rocD ornithine aminotransferase PfGW456L13_4910 PfGW456L13_494

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