GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Desulfacinum infernum DSM 9756

Best path

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

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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component BUB04_RS03450
AO353_03050 ABC transporter for L-Citrulline, permease component 1 BUB04_RS06475 BUB04_RS06465
AO353_03045 ABC transporter for L-Citrulline, permease component 2 BUB04_RS05850 BUB04_RS13795
AO353_03040 ABC transporter for L-Citrulline, ATPase component BUB04_RS05855 BUB04_RS10875
arcB ornithine carbamoyltransferase BUB04_RS11055 BUB04_RS04235
arcC carbamate kinase BUB04_RS05565
rocD ornithine aminotransferase BUB04_RS10885 BUB04_RS02225
rocA 1-pyrroline-5-carboxylate dehydrogenase BUB04_RS13170 BUB04_RS05780
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase BUB04_RS11050 BUB04_RS02225
astD succinylglutamate semialdehyde dehydrogenase BUB04_RS13170 BUB04_RS04110
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase BUB04_RS03720 BUB04_RS00235
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase BUB04_RS04110 BUB04_RS05780
davT 5-aminovalerate aminotransferase BUB04_RS02225 BUB04_RS08145
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BUB04_RS03725 BUB04_RS07705
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BUB04_RS17405 BUB04_RS00230
gabD succinate semialdehyde dehydrogenase BUB04_RS04110 BUB04_RS05780
gabT gamma-aminobutyrate transaminase BUB04_RS10885 BUB04_RS02225
gcdG succinyl-CoA:glutarate CoA-transferase BUB04_RS05220 BUB04_RS08370
gcdH glutaryl-CoA dehydrogenase BUB04_RS03730 BUB04_RS05240
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BUB04_RS00730
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) BUB04_RS08170 BUB04_RS06460
patD gamma-aminobutyraldehyde dehydrogenase BUB04_RS04110 BUB04_RS05780
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC BUB04_RS17555
prdF proline racemase
PRO3 pyrroline-5-carboxylate reductase BUB04_RS10375
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1 BUB04_RS06475 BUB04_RS10880
PS417_17600 ABC transporter for L-Citrulline, permease component 2 BUB04_RS06465 BUB04_RS09975
PS417_17605 ABC transporter for L-Citrulline, ATPase component BUB04_RS05855 BUB04_RS14565
puo putrescine oxidase
put1 proline dehydrogenase BUB04_RS13170 BUB04_RS16575
putA L-glutamate 5-semialdeyde dehydrogenase BUB04_RS13170 BUB04_RS05780
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BUB04_RS04110 BUB04_RS05780
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase

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