GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Haloglycomyces albus DSM 45210

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, 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 (23 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 HALAL_RS0102765 HALAL_RS0104120
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component HALAL_RS0102760 HALAL_RS0113980
arcB ornithine carbamoyltransferase HALAL_RS0112705 HALAL_RS0114950
arcC carbamate kinase
ocd ornithine cyclodeaminase
put1 proline dehydrogenase HALAL_RS0107260
putA L-glutamate 5-semialdeyde dehydrogenase HALAL_RS0103000 HALAL_RS0112015
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase HALAL_RS0112700 HALAL_RS0102620
astD succinylglutamate semialdehyde dehydrogenase HALAL_RS0112015 HALAL_RS0110770
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase HALAL_RS0107190 HALAL_RS0108855
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase HALAL_RS0102625 HALAL_RS0112015
davT 5-aminovalerate aminotransferase HALAL_RS0102620 HALAL_RS0112700
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HALAL_RS0110635
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HALAL_RS0108355 HALAL_RS0110635
gabD succinate semialdehyde dehydrogenase HALAL_RS0102625 HALAL_RS0110770
gabT gamma-aminobutyrate transaminase HALAL_RS0102620 HALAL_RS0113645
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase HALAL_RS0107635 HALAL_RS0104340
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
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) HALAL_RS0112700 HALAL_RS0102620
patD gamma-aminobutyraldehyde dehydrogenase HALAL_RS0112015 HALAL_RS0110770
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
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1 HALAL_RS0102765 HALAL_RS0104125
PS417_17600 ABC transporter for L-Citrulline, permease component 2
PS417_17605 ABC transporter for L-Citrulline, ATPase component HALAL_RS0102760 HALAL_RS0113980
puo putrescine oxidase
puuA glutamate-putrescine ligase HALAL_RS0111445
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase HALAL_RS0112015 HALAL_RS0110770
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase HALAL_RS0103000 HALAL_RS0112015
rocD ornithine aminotransferase HALAL_RS0102620 HALAL_RS0113645

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 Apr 09 2024. 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