GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Acidovorax caeni R-24608

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component BN2503_RS00930
AO353_03050 ABC transporter for L-Citrulline, permease component 1 BN2503_RS00925 BN2503_RS00885
AO353_03045 ABC transporter for L-Citrulline, permease component 2 BN2503_RS00920 BN2503_RS00885
AO353_03040 ABC transporter for L-Citrulline, ATPase component BN2503_RS00915 BN2503_RS00880
arcB ornithine carbamoyltransferase BN2503_RS11435 BN2503_RS04795
arcC carbamate kinase
rocD ornithine aminotransferase BN2503_RS03550 BN2503_RS11430
PRO3 pyrroline-5-carboxylate reductase BN2503_RS18030 BN2503_RS19795
put1 proline dehydrogenase BN2503_RS05615
putA L-glutamate 5-semialdeyde dehydrogenase BN2503_RS05615 BN2503_RS03555
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase BN2503_RS11430 BN2503_RS04745
astD succinylglutamate semialdehyde dehydrogenase BN2503_RS02410 BN2503_RS05615
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase BN2503_RS17070 BN2503_RS12305
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase BN2503_RS02410 BN2503_RS03525
davT 5-aminovalerate aminotransferase BN2503_RS11430 BN2503_RS04745
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BN2503_RS05070 BN2503_RS12155
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BN2503_RS10700 BN2503_RS06880
gabD succinate semialdehyde dehydrogenase BN2503_RS02410 BN2503_RS03525
gabT gamma-aminobutyrate transaminase BN2503_RS03550 BN2503_RS11430
gcdG succinyl-CoA:glutarate CoA-transferase BN2503_RS01975 BN2503_RS09355
gcdH glutaryl-CoA dehydrogenase BN2503_RS01970 BN2503_RS15695
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 BN2503_RS13850
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) BN2503_RS03550 BN2503_RS11430
patD gamma-aminobutyraldehyde dehydrogenase BN2503_RS03525 BN2503_RS02410
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 BN2503_RS00930
PS417_17595 ABC transporter for L-Citrulline, permease component 1 BN2503_RS00925 BN2503_RS00885
PS417_17600 ABC transporter for L-Citrulline, permease component 2 BN2503_RS00920 BN2503_RS00885
PS417_17605 ABC transporter for L-Citrulline, ATPase component BN2503_RS00915 BN2503_RS00880
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BN2503_RS03525 BN2503_RS02410
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase BN2503_RS05615 BN2503_RS03555

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