GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Dechlorosoma suillum PS

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA

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 Dsui_0636 Dsui_0637
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component Dsui_0638 Dsui_2068
arcB ornithine carbamoyltransferase Dsui_3249
arcC carbamate kinase
rocD ornithine aminotransferase Dsui_3250 Dsui_0023
rocA 1-pyrroline-5-carboxylate dehydrogenase Dsui_0437 Dsui_1464
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase Dsui_3250 Dsui_0023
astD succinylglutamate semialdehyde dehydrogenase Dsui_0105 Dsui_0437
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Dsui_0976 Dsui_3239
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase Dsui_0437 Dsui_0105
davT 5-aminovalerate aminotransferase Dsui_3250 Dsui_0023
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Dsui_1378 Dsui_0323
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Dsui_0318 Dsui_2330
gabD succinate semialdehyde dehydrogenase Dsui_0437 Dsui_0105
gabT gamma-aminobutyrate transaminase Dsui_3250 Dsui_0023
gcdG succinyl-CoA:glutarate CoA-transferase Dsui_0037 Dsui_1115
gcdH glutaryl-CoA dehydrogenase Dsui_3369 Dsui_0977
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Dsui_2329
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase Dsui_1245
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) Dsui_3250 Dsui_0023
patD gamma-aminobutyraldehyde dehydrogenase Dsui_0105 Dsui_1464
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 Dsui_0602
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1 Dsui_0637
PS417_17600 ABC transporter for L-Citrulline, permease component 2
PS417_17605 ABC transporter for L-Citrulline, ATPase component Dsui_0638 Dsui_2877
puo putrescine oxidase
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase Dsui_0437 Dsui_1464
puuA glutamate-putrescine ligase Dsui_1048
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Dsui_1464 Dsui_0105
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Dsui_3391 Dsui_3244

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