GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Paraburkholderia phymatum STM815

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD

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 BPHY_RS19095 BPHY_RS09055
AO353_03050 ABC transporter for L-Citrulline, permease component 1 BPHY_RS11015 BPHY_RS09110
AO353_03045 ABC transporter for L-Citrulline, permease component 2 BPHY_RS09105 BPHY_RS11020
AO353_03040 ABC transporter for L-Citrulline, ATPase component BPHY_RS09100 BPHY_RS11025
arcB ornithine carbamoyltransferase BPHY_RS32075 BPHY_RS02660
arcC carbamate kinase BPHY_RS32070
odc L-ornithine decarboxylase BPHY_RS32090 BPHY_RS11130
puuA glutamate-putrescine ligase BPHY_RS18060 BPHY_RS38400
puuB gamma-glutamylputrescine oxidase BPHY_RS18185 BPHY_RS32820
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BPHY_RS18040 BPHY_RS34150
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase BPHY_RS18055 BPHY_RS34660
gabT gamma-aminobutyrate transaminase BPHY_RS18065 BPHY_RS23215
gabD succinate semialdehyde dehydrogenase BPHY_RS27205 BPHY_RS24330
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) BPHY_RS09085 BPHY_RS09080
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) BPHY_RS09080 BPHY_RS09085
astC succinylornithine transaminase BPHY_RS09090 BPHY_RS02980
astD succinylglutamate semialdehyde dehydrogenase BPHY_RS09075 BPHY_RS19265
astE succinylglutamate desuccinylase BPHY_RS09065
atoB acetyl-CoA C-acetyltransferase BPHY_RS04915 BPHY_RS04940
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase BPHY_RS24330 BPHY_RS16380
davT 5-aminovalerate aminotransferase BPHY_RS24335 BPHY_RS23215
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BPHY_RS13655 BPHY_RS24290
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BPHY_RS01920 BPHY_RS35840
gcdG succinyl-CoA:glutarate CoA-transferase BPHY_RS08225 BPHY_RS31935
gcdH glutaryl-CoA dehydrogenase BPHY_RS12365 BPHY_RS18015
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BPHY_RS00525
ocd ornithine cyclodeaminase
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) BPHY_RS18065 BPHY_RS32700
patD gamma-aminobutyraldehyde dehydrogenase BPHY_RS18040 BPHY_RS16780
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase BPHY_RS16950 BPHY_RS23455
PRO3 pyrroline-5-carboxylate reductase BPHY_RS12780
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component BPHY_RS19095 BPHY_RS11010
PS417_17595 ABC transporter for L-Citrulline, permease component 1 BPHY_RS11015 BPHY_RS09110
PS417_17600 ABC transporter for L-Citrulline, permease component 2 BPHY_RS11020 BPHY_RS09105
PS417_17605 ABC transporter for L-Citrulline, ATPase component BPHY_RS09100 BPHY_RS37105
puo putrescine oxidase
put1 proline dehydrogenase BPHY_RS15380 BPHY_RS29565
putA L-glutamate 5-semialdeyde dehydrogenase BPHY_RS15380 BPHY_RS23615
rocA 1-pyrroline-5-carboxylate dehydrogenase BPHY_RS15380 BPHY_RS23615
rocD ornithine aminotransferase BPHY_RS24335 BPHY_RS23215

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