GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Pedobacter sp. GW460-11-11-14-LB5

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 (27 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 CA265_RS16020 CA265_RS04175
citrullinase putative citrullinase CA265_RS10475 CA265_RS15465
rocD ornithine aminotransferase CA265_RS15205 CA265_RS18530
PRO3 pyrroline-5-carboxylate reductase CA265_RS18505
put1 proline dehydrogenase CA265_RS11605
putA L-glutamate 5-semialdeyde dehydrogenase CA265_RS16605 CA265_RS14635
Alternative steps:
arcB ornithine carbamoyltransferase CA265_RS14660 CA265_RS18520
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase CA265_RS15205 CA265_RS18530
astD succinylglutamate semialdehyde dehydrogenase CA265_RS24850 CA265_RS19780
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase CA265_RS06590 CA265_RS17585
davD glutarate semialdehyde dehydrogenase CA265_RS14635 CA265_RS24850
davT 5-aminovalerate aminotransferase CA265_RS18530 CA265_RS15205
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CA265_RS20005 CA265_RS09125
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CA265_RS17590 CA265_RS07715
gabD succinate semialdehyde dehydrogenase CA265_RS24850 CA265_RS01080
gabT gamma-aminobutyrate transaminase CA265_RS14455 CA265_RS18530
gcdG succinyl-CoA:glutarate CoA-transferase CA265_RS08550
gcdH glutaryl-CoA dehydrogenase CA265_RS09630 CA265_RS14465
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) CA265_RS19300
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase
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) CA265_RS15205 CA265_RS18530
patD gamma-aminobutyraldehyde dehydrogenase CA265_RS14635 CA265_RS24850
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase CA265_RS05710
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 CA265_RS16020 CA265_RS07485
puo putrescine oxidase
puuA glutamate-putrescine ligase CA265_RS24865
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase CA265_RS14635 CA265_RS24850
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase CA265_RS24855
rocA 1-pyrroline-5-carboxylate dehydrogenase CA265_RS16605 CA265_RS14635

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