GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Pseudomonas stutzeri RCH2

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component Psest_0138
AO353_03050 ABC transporter for L-Citrulline, permease component 1 Psest_0137 Psest_0018
AO353_03045 ABC transporter for L-Citrulline, permease component 2 Psest_0136 Psest_0018
AO353_03040 ABC transporter for L-Citrulline, ATPase component Psest_0139 Psest_0016
arcB ornithine carbamoyltransferase Psest_0271 Psest_1291
arcC carbamate kinase Psest_0270
odc L-ornithine decarboxylase Psest_3350 Psest_2075
puuA glutamate-putrescine ligase Psest_4288 Psest_4286
puuB gamma-glutamylputrescine oxidase Psest_1966 Psest_3795
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Psest_4305 Psest_0905
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Psest_4287
gabT gamma-aminobutyrate transaminase Psest_4285 Psest_3653
gabD succinate semialdehyde dehydrogenase Psest_4237 Psest_3654
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase Psest_2719 Psest_3653
astD succinylglutamate semialdehyde dehydrogenase Psest_3654 Psest_4305
astE succinylglutamate desuccinylase Psest_2717
atoB acetyl-CoA C-acetyltransferase Psest_1076 Psest_2446
citrullinase putative citrullinase Psest_4290
davD glutarate semialdehyde dehydrogenase Psest_4237 Psest_3654
davT 5-aminovalerate aminotransferase Psest_3653 Psest_2719
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Psest_2437 Psest_3109
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Psest_2654 Psest_4235
gcdG succinyl-CoA:glutarate CoA-transferase Psest_3829 Psest_2660
gcdH glutaryl-CoA dehydrogenase Psest_3830 Psest_2440
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Psest_0232
ocd ornithine cyclodeaminase
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) Psest_4285 Psest_4306
patD gamma-aminobutyraldehyde dehydrogenase Psest_4305 Psest_2634
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
PRO3 pyrroline-5-carboxylate reductase Psest_0283
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component Psest_0138
PS417_17595 ABC transporter for L-Citrulline, permease component 1 Psest_0137 Psest_0018
PS417_17600 ABC transporter for L-Citrulline, permease component 2 Psest_0136 Psest_0137
PS417_17605 ABC transporter for L-Citrulline, ATPase component Psest_0139 Psest_0016
puo putrescine oxidase
put1 proline dehydrogenase Psest_3079
putA L-glutamate 5-semialdeyde dehydrogenase Psest_3079 Psest_0375
rocA 1-pyrroline-5-carboxylate dehydrogenase Psest_3079 Psest_0375
rocD ornithine aminotransferase Psest_2719 Psest_3653

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