GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Pseudomonas benzenivorans DSM 8628

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component BLS63_RS26095 BLS63_RS08500
AO353_03050 ABC transporter for L-Citrulline, permease component 1 BLS63_RS26100 BLS63_RS01125
AO353_03045 ABC transporter for L-Citrulline, permease component 2 BLS63_RS26105 BLS63_RS24450
AO353_03040 ABC transporter for L-Citrulline, ATPase component BLS63_RS26115 BLS63_RS01135
arcB ornithine carbamoyltransferase BLS63_RS10650 BLS63_RS23235
arcC carbamate kinase BLS63_RS10655
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) BLS63_RS19260 BLS63_RS19265
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) BLS63_RS19265 BLS63_RS19260
astC succinylornithine transaminase BLS63_RS19255 BLS63_RS01095
astD succinylglutamate semialdehyde dehydrogenase BLS63_RS19270 BLS63_RS15725
astE succinylglutamate desuccinylase BLS63_RS19285
Alternative steps:
atoB acetyl-CoA C-acetyltransferase BLS63_RS22810 BLS63_RS21120
citrullinase putative citrullinase BLS63_RS16685
davD glutarate semialdehyde dehydrogenase BLS63_RS26230 BLS63_RS15725
davT 5-aminovalerate aminotransferase BLS63_RS01095 BLS63_RS26240
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLS63_RS21705 BLS63_RS07890
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLS63_RS07890 BLS63_RS21115
gabD succinate semialdehyde dehydrogenase BLS63_RS26230 BLS63_RS15725
gabT gamma-aminobutyrate transaminase BLS63_RS08505 BLS63_RS16660
gcdG succinyl-CoA:glutarate CoA-transferase BLS63_RS14580 BLS63_RS17670
gcdH glutaryl-CoA dehydrogenase BLS63_RS14585 BLS63_RS24330
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BLS63_RS24405
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase BLS63_RS22540 BLS63_RS01145
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) BLS63_RS16660 BLS63_RS08505
patD gamma-aminobutyraldehyde dehydrogenase BLS63_RS09095 BLS63_RS09120
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 BLS63_RS16225
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component BLS63_RS26095 BLS63_RS08500
PS417_17595 ABC transporter for L-Citrulline, permease component 1 BLS63_RS26100 BLS63_RS01125
PS417_17600 ABC transporter for L-Citrulline, permease component 2 BLS63_RS26105 BLS63_RS24450
PS417_17605 ABC transporter for L-Citrulline, ATPase component BLS63_RS26115 BLS63_RS24435
puo putrescine oxidase
put1 proline dehydrogenase BLS63_RS22035
putA L-glutamate 5-semialdeyde dehydrogenase BLS63_RS22035 BLS63_RS03170
puuA glutamate-putrescine ligase BLS63_RS16675 BLS63_RS16665
puuB gamma-glutamylputrescine oxidase BLS63_RS17215 BLS63_RS19080
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BLS63_RS19060 BLS63_RS08515
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase BLS63_RS16670
rocA 1-pyrroline-5-carboxylate dehydrogenase BLS63_RS22035 BLS63_RS03170
rocD ornithine aminotransferase BLS63_RS07545 BLS63_RS01095

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