GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Thiothrix lacustris DSM 21227

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component Q394_RS0118295
AO353_03050 ABC transporter for L-Citrulline, permease component 1 Q394_RS0118290 Q394_RS0118285
AO353_03045 ABC transporter for L-Citrulline, permease component 2 Q394_RS0118285 Q394_RS0118290
AO353_03040 ABC transporter for L-Citrulline, ATPase component Q394_RS0106625 Q394_RS0103835
citrullinase putative citrullinase Q394_RS0100130
rocD ornithine aminotransferase Q394_RS0113995
rocA 1-pyrroline-5-carboxylate dehydrogenase Q394_RS0111975 Q394_RS0104930
Alternative steps:
arcB ornithine carbamoyltransferase Q394_RS0113990 Q394_RS0108935
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase Q394_RS0113995 Q394_RS0104770
astD succinylglutamate semialdehyde dehydrogenase Q394_RS0117580 Q394_RS0111975
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Q394_RS0118420 Q394_RS0100445
davD glutarate semialdehyde dehydrogenase Q394_RS0117580 Q394_RS0111975
davT 5-aminovalerate aminotransferase Q394_RS0113995 Q394_RS0104770
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Q394_RS0103080 Q394_RS0112850
gabD succinate semialdehyde dehydrogenase Q394_RS0117580 Q394_RS0111975
gabT gamma-aminobutyrate transaminase Q394_RS0113995 Q394_RS0111125
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
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) Q394_RS0113995 Q394_RS0111125
patD gamma-aminobutyraldehyde dehydrogenase Q394_RS0111975 Q394_RS0104930
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 Q394_RS0112940
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component Q394_RS0118295
PS417_17595 ABC transporter for L-Citrulline, permease component 1 Q394_RS0118290 Q394_RS0118285
PS417_17600 ABC transporter for L-Citrulline, permease component 2 Q394_RS0118285
PS417_17605 ABC transporter for L-Citrulline, ATPase component Q394_RS0106625 Q394_RS0103835
puo putrescine oxidase
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase Q394_RS0111975 Q394_RS0104930
puuA glutamate-putrescine ligase Q394_RS0105560
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Q394_RS0104930 Q394_RS0111975
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase

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