GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Dokdonella koreensis DS-123

Best path

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

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 (25 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 I596_RS09325 I596_RS02480
citrullinase putative citrullinase I596_RS08295
rocD ornithine aminotransferase I596_RS12880 I596_RS03965
PRO3 pyrroline-5-carboxylate reductase I596_RS03265
put1 proline dehydrogenase I596_RS14475
putA L-glutamate 5-semialdeyde dehydrogenase I596_RS14475 I596_RS04140
Alternative steps:
arcB ornithine carbamoyltransferase I596_RS10160 I596_RS03730
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase I596_RS03960 I596_RS12880
astD succinylglutamate semialdehyde dehydrogenase I596_RS02225 I596_RS04570
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase I596_RS05370 I596_RS06325
davD glutarate semialdehyde dehydrogenase I596_RS02225 I596_RS04140
davT 5-aminovalerate aminotransferase I596_RS03960 I596_RS12880
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase I596_RS12940 I596_RS02240
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase I596_RS06330 I596_RS02240
gabD succinate semialdehyde dehydrogenase I596_RS04570 I596_RS02225
gabT gamma-aminobutyrate transaminase I596_RS12880 I596_RS03960
gcdG succinyl-CoA:glutarate CoA-transferase I596_RS10325
gcdH glutaryl-CoA dehydrogenase I596_RS15145 I596_RS15670
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
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) I596_RS12880 I596_RS03960
patD gamma-aminobutyraldehyde dehydrogenase I596_RS04570 I596_RS02225
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 I596_RS09325 I596_RS02480
puo putrescine oxidase
puuA glutamate-putrescine ligase I596_RS17215
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase I596_RS04570 I596_RS02225
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase I596_RS03770
rocA 1-pyrroline-5-carboxylate dehydrogenase I596_RS14475 I596_RS04140

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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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