GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Sphingomonas koreensis DSMZ 15582

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA

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 (26 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_03050 ABC transporter for L-Citrulline, permease component 1
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component Ga0059261_3653 Ga0059261_2293
citrullinase putative citrullinase Ga0059261_1979
rocD ornithine aminotransferase Ga0059261_3205 Ga0059261_4131
PRO3 pyrroline-5-carboxylate reductase Ga0059261_3321 Ga0059261_3808
put1 proline dehydrogenase Ga0059261_3926
putA L-glutamate 5-semialdeyde dehydrogenase Ga0059261_3926 Ga0059261_3374
Alternative steps:
arcB ornithine carbamoyltransferase Ga0059261_3206 Ga0059261_0076
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) Ga0059261_3996
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) Ga0059261_3996
astC succinylornithine transaminase Ga0059261_3205 Ga0059261_4131
astD succinylglutamate semialdehyde dehydrogenase Ga0059261_4132 Ga0059261_1495
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Ga0059261_0982 Ga0059261_2888
davD glutarate semialdehyde dehydrogenase Ga0059261_0516 Ga0059261_1680
davT 5-aminovalerate aminotransferase Ga0059261_4131 Ga0059261_3205
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Ga0059261_3685 Ga0059261_2668
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Ga0059261_2816 Ga0059261_0837
gabD succinate semialdehyde dehydrogenase Ga0059261_1006 Ga0059261_1680
gabT gamma-aminobutyrate transaminase Ga0059261_4131 Ga0059261_3205
gcdG succinyl-CoA:glutarate CoA-transferase Ga0059261_2166 Ga0059261_2807
gcdH glutaryl-CoA dehydrogenase Ga0059261_2164 Ga0059261_4052
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 Ga0059261_3753
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) Ga0059261_4131 Ga0059261_3205
patD gamma-aminobutyraldehyde dehydrogenase Ga0059261_3374 Ga0059261_1680
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1
PS417_17600 ABC transporter for L-Citrulline, permease component 2
PS417_17605 ABC transporter for L-Citrulline, ATPase component Ga0059261_3653 Ga0059261_0341
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Ga0059261_3374 Ga0059261_1680
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase Ga0059261_3926 Ga0059261_3374

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.

Links

Downloads

Related tools

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