GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Pseudomonas fluorescens FW300-N2E3

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

Rules

Overview: Citrulline can be catabolized via ornithine carbamoyltransferase in reverse (PMID:3129535). Genetic evidence suggests that some bacteria use a putative citrullinase (EC 3.5.1.20) 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 AO353_03055 AO353_27970
AO353_03050 ABC transporter for L-Citrulline, permease component 1 AO353_03050 AO353_27975
AO353_03045 ABC transporter for L-Citrulline, permease component 2 AO353_03045 AO353_27980
AO353_03040 ABC transporter for L-Citrulline, ATPase component AO353_03040 AO353_27990
arcB ornithine carbamoyltransferase AO353_03475 AO353_04155
arcC carbamate kinase AO353_03480
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) AO353_03020 AO353_27915
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) AO353_03015 AO353_25630
astC succinylornithine transaminase AO353_03025 AO353_10500
astD succinylglutamate semialdehyde dehydrogenase AO353_03010 AO353_09195
astE succinylglutamate desuccinylase AO353_02995
Alternative steps:
atoB acetyl-CoA C-acetyltransferase AO353_25685 AO353_27945
citrullinase putative citrullinase AO353_25635 AO353_11910
davD glutarate semialdehyde dehydrogenase AO353_11505 AO353_28230
davT 5-aminovalerate aminotransferase AO353_11510 AO353_28215
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AO353_25675 AO353_00510
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AO353_00510 AO353_27535
gabD succinate semialdehyde dehydrogenase AO353_11505 AO353_28230
gabT gamma-aminobutyrate transaminase AO353_08585 AO353_15040
gcdG succinyl-CoA:glutarate CoA-transferase AO353_11105 AO353_23060
gcdH glutaryl-CoA dehydrogenase AO353_11100 AO353_20350
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase AO353_25185
odc L-ornithine decarboxylase AO353_05445 AO353_23560
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) AO353_08585 AO353_15040
patD gamma-aminobutyraldehyde dehydrogenase AO353_04290 AO353_04265
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase AO353_14925 AO353_14880
PRO3 pyrroline-5-carboxylate reductase AO353_08165
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component AO353_25660 AO353_01540
PS417_17595 ABC transporter for L-Citrulline, permease component 1 AO353_25655 AO353_01535
PS417_17600 ABC transporter for L-Citrulline, permease component 2 AO353_25650 AO353_01530
PS417_17605 ABC transporter for L-Citrulline, ATPase component AO353_25645 AO353_16950
puo putrescine oxidase
put1 proline dehydrogenase AO353_12810
putA L-glutamate 5-semialdeyde dehydrogenase AO353_12810 AO353_05300
puuA glutamate-putrescine ligase AO353_08595 AO353_29300
puuB gamma-glutamylputrescine oxidase AO353_20720 AO353_29290
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AO353_09195 AO353_29295
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase AO353_29305
rocA 1-pyrroline-5-carboxylate dehydrogenase AO353_12810 AO353_05300
rocD ornithine aminotransferase AO353_15640 AO353_28215

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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