GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Rhodanobacter denitrificans FW104-10B01

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, 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
AO353_03050 ABC transporter for L-Citrulline, permease component 1
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component LRK54_RS14735 LRK54_RS15720
citrullinase putative citrullinase LRK54_RS00340
rocD ornithine aminotransferase LRK54_RS04500 LRK54_RS03035
PRO3 pyrroline-5-carboxylate reductase LRK54_RS04260
put1 proline dehydrogenase LRK54_RS07135
putA L-glutamate 5-semialdeyde dehydrogenase LRK54_RS07135 LRK54_RS04485
Alternative steps:
arcB ornithine carbamoyltransferase LRK54_RS02415 LRK54_RS04220
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase LRK54_RS06590 LRK54_RS04500
astD succinylglutamate semialdehyde dehydrogenase LRK54_RS02575 LRK54_RS04485
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase LRK54_RS15265 LRK54_RS00050
davD glutarate semialdehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
davT 5-aminovalerate aminotransferase LRK54_RS04500 LRK54_RS06590
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase LRK54_RS15165 LRK54_RS16925
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase LRK54_RS00055 LRK54_RS16925
gabD succinate semialdehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
gabT gamma-aminobutyrate transaminase LRK54_RS04500 LRK54_RS04150
gcdG succinyl-CoA:glutarate CoA-transferase LRK54_RS07425
gcdH glutaryl-CoA dehydrogenase LRK54_RS02070 LRK54_RS02105
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
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) LRK54_RS04500 LRK54_RS04150
patD gamma-aminobutyraldehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
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
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 LRK54_RS14735 LRK54_RS15720
puo putrescine oxidase
puuA glutamate-putrescine ligase LRK54_RS08105
puuB gamma-glutamylputrescine oxidase LRK54_RS18070
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase LRK54_RS07135 LRK54_RS04485

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