GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Stutzerimonas stutzeri A1501

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component PST_RS20435 PST_RS11840
AO353_03050 ABC transporter for L-Citrulline, permease component 1 PST_RS20440 PST_RS11845
AO353_03045 ABC transporter for L-Citrulline, permease component 2 PST_RS20445 PST_RS11845
AO353_03040 ABC transporter for L-Citrulline, ATPase component PST_RS20430 PST_RS11850
arcB ornithine carbamoyltransferase PST_RS03485 PST_RS19805
arcC carbamate kinase PST_RS03480 PST_RS19810
odc L-ornithine decarboxylase PST_RS05085 PST_RS11335
puuA glutamate-putrescine ligase PST_RS00325 PST_RS00335
puuB gamma-glutamylputrescine oxidase PST_RS11935 PST_RS02480
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PST_RS00240 PST_RS08835
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase PST_RS00330
gabT gamma-aminobutyrate transaminase PST_RS00340 PST_RS03780
gabD succinate semialdehyde dehydrogenase PST_RS00500 PST_RS03775
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase PST_RS08350 PST_RS03780
astD succinylglutamate semialdehyde dehydrogenase PST_RS00240 PST_RS03775
astE succinylglutamate desuccinylase PST_RS08360
atoB acetyl-CoA C-acetyltransferase PST_RS03530 PST_RS16155
citrullinase putative citrullinase PST_RS00315
davD glutarate semialdehyde dehydrogenase PST_RS00500 PST_RS03775
davT 5-aminovalerate aminotransferase PST_RS03780 PST_RS08350
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PST_RS09740 PST_RS06175
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PST_RS08735 PST_RS00510
gcdG succinyl-CoA:glutarate CoA-transferase PST_RS02290 PST_RS08605
gcdH glutaryl-CoA dehydrogenase PST_RS02285 PST_RS09725
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) PST_RS19980
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) PST_RS00340 PST_RS00235
patD gamma-aminobutyraldehyde dehydrogenase PST_RS00240 PST_RS08835
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 PST_RS19745
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component PST_RS20435
PS417_17595 ABC transporter for L-Citrulline, permease component 1 PST_RS20440 PST_RS00085
PS417_17600 ABC transporter for L-Citrulline, permease component 2 PST_RS20445 PST_RS11845
PS417_17605 ABC transporter for L-Citrulline, ATPase component PST_RS20430 PST_RS11850
puo putrescine oxidase
put1 proline dehydrogenase PST_RS06320
putA L-glutamate 5-semialdeyde dehydrogenase PST_RS06320 PST_RS00500
rocA 1-pyrroline-5-carboxylate dehydrogenase PST_RS06320 PST_RS00500
rocD ornithine aminotransferase PST_RS03780 PST_RS08350

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