GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Methylocapsa aurea KYG

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, 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 DL86_RS15435 DL86_RS12660
AO353_03050 ABC transporter for L-Citrulline, permease component 1 DL86_RS08970
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component DL86_RS08980 DL86_RS09915
arcB ornithine carbamoyltransferase DL86_RS01860 DL86_RS03635
arcC carbamate kinase
rocD ornithine aminotransferase DL86_RS06885 DL86_RS06705
PRO3 pyrroline-5-carboxylate reductase DL86_RS07785
put1 proline dehydrogenase DL86_RS17780
putA L-glutamate 5-semialdeyde dehydrogenase DL86_RS17780 DL86_RS14335
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase DL86_RS01865 DL86_RS06885
astD succinylglutamate semialdehyde dehydrogenase DL86_RS17780 DL86_RS09925
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase DL86_RS05200 DL86_RS10295
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase DL86_RS14335 DL86_RS09925
davT 5-aminovalerate aminotransferase DL86_RS01865 DL86_RS06705
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase DL86_RS15400 DL86_RS06940
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase DL86_RS06940 DL86_RS07960
gabD succinate semialdehyde dehydrogenase DL86_RS14335 DL86_RS03210
gabT gamma-aminobutyrate transaminase DL86_RS13850 DL86_RS06885
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase DL86_RS07065 DL86_RS00105
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 DL86_RS09855 DL86_RS13630
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) DL86_RS13850 DL86_RS01865
patD gamma-aminobutyraldehyde dehydrogenase DL86_RS14335 DL86_RS09925
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 DL86_RS12660
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 DL86_RS08980 DL86_RS02760
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase DL86_RS14335 DL86_RS09925
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase DL86_RS17780 DL86_RS14335

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