GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Pseudomonas fluorescens FW300-N2E2

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 (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 Pf6N2E2_5660 Pf6N2E2_1098
AO353_03050 ABC transporter for L-Citrulline, permease component 1 Pf6N2E2_5661 Pf6N2E2_2959
AO353_03045 ABC transporter for L-Citrulline, permease component 2 Pf6N2E2_5662 Pf6N2E2_3858
AO353_03040 ABC transporter for L-Citrulline, ATPase component Pf6N2E2_5663 Pf6N2E2_2962
arcB ornithine carbamoyltransferase Pf6N2E2_2909 Pf6N2E2_5579
arcC carbamate kinase Pf6N2E2_2910
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) Pf6N2E2_5666 Pf6N2E2_2180
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) Pf6N2E2_5667 Pf6N2E2_2181
astC succinylornithine transaminase Pf6N2E2_5665 Pf6N2E2_5326
astD succinylglutamate semialdehyde dehydrogenase Pf6N2E2_5668 Pf6N2E2_1370
astE succinylglutamate desuccinylase Pf6N2E2_5671
Alternative steps:
atoB acetyl-CoA C-acetyltransferase Pf6N2E2_2113 Pf6N2E2_1145
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase Pf6N2E2_4014 Pf6N2E2_368
davT 5-aminovalerate aminotransferase Pf6N2E2_4013 Pf6N2E2_373
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf6N2E2_1147 Pf6N2E2_1834
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf6N2E2_2290 Pf6N2E2_1922
gabD succinate semialdehyde dehydrogenase Pf6N2E2_4014 Pf6N2E2_1919
gabT gamma-aminobutyrate transaminase Pf6N2E2_4512 Pf6N2E2_4013
gcdG succinyl-CoA:glutarate CoA-transferase Pf6N2E2_4035 Pf6N2E2_3139
gcdH glutaryl-CoA dehydrogenase Pf6N2E2_4036 Pf6N2E2_2191
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Pf6N2E2_261
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase Pf6N2E2_3334
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) Pf6N2E2_4512 Pf6N2E2_1742
patD gamma-aminobutyraldehyde dehydrogenase Pf6N2E2_3131 Pf6N2E2_3126
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Pf6N2E2_681 Pf6N2E2_671
PRO3 pyrroline-5-carboxylate reductase Pf6N2E2_4600
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component Pf6N2E2_2958 Pf6N2E2_5660
PS417_17595 ABC transporter for L-Citrulline, permease component 1 Pf6N2E2_2959 Pf6N2E2_5661
PS417_17600 ABC transporter for L-Citrulline, permease component 2 Pf6N2E2_2960 Pf6N2E2_5662
PS417_17605 ABC transporter for L-Citrulline, ATPase component Pf6N2E2_2962 Pf6N2E2_5663
puo putrescine oxidase
put1 proline dehydrogenase Pf6N2E2_3685
putA L-glutamate 5-semialdeyde dehydrogenase Pf6N2E2_3685 Pf6N2E2_3298
puuA glutamate-putrescine ligase Pf6N2E2_4509 Pf6N2E2_4511
puuB gamma-glutamylputrescine oxidase Pf6N2E2_80 Pf6N2E2_4388
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Pf6N2E2_4383 Pf6N2E2_1381
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Pf6N2E2_4510
rocA 1-pyrroline-5-carboxylate dehydrogenase Pf6N2E2_3685 Pf6N2E2_3298
rocD ornithine aminotransferase Pf6N2E2_5326 Pf6N2E2_373

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