GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Azohydromonas australica DSM 1124

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component H537_RS0108525
AO353_03050 ABC transporter for L-Citrulline, permease component 1 H537_RS0108530 H537_RS41215
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component H537_RS0128690 H537_RS0107725
arcB ornithine carbamoyltransferase H537_RS0120485 H537_RS0100960
arcC carbamate kinase
ocd ornithine cyclodeaminase H537_RS0133445
put1 proline dehydrogenase H537_RS0124445 H537_RS44845
putA L-glutamate 5-semialdeyde dehydrogenase H537_RS0124445 H537_RS44845
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase H537_RS0137245 H537_RS0120480
astD succinylglutamate semialdehyde dehydrogenase H537_RS0110805 H537_RS0121615
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase H537_RS0122115 H537_RS0129600
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase H537_RS0138620 H537_RS0120085
davT 5-aminovalerate aminotransferase H537_RS0120050 H537_RS0137245
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H537_RS0100790 H537_RS0111045
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H537_RS0132195 H537_RS0116855
gabD succinate semialdehyde dehydrogenase H537_RS0101950 H537_RS0138620
gabT gamma-aminobutyrate transaminase H537_RS0136115 H537_RS0120050
gcdG succinyl-CoA:glutarate CoA-transferase H537_RS0123940 H537_RS44370
gcdH glutaryl-CoA dehydrogenase H537_RS0120055 H537_RS0115055
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H537_RS0114715
odc L-ornithine decarboxylase H537_RS0110665
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) H537_RS0136115 H537_RS0136130
patD gamma-aminobutyraldehyde dehydrogenase H537_RS0136110 H537_RS0122420
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 H537_RS0134655
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1 H537_RS0107730 H537_RS0128685
PS417_17600 ABC transporter for L-Citrulline, permease component 2
PS417_17605 ABC transporter for L-Citrulline, ATPase component H537_RS0107725 H537_RS0128690
puo putrescine oxidase
puuA glutamate-putrescine ligase H537_RS0136120 H537_RS0125925
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase H537_RS0122420 H537_RS0136110
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase H537_RS0136125 H537_RS0129405
rocA 1-pyrroline-5-carboxylate dehydrogenase H537_RS0124445 H537_RS44845
rocD ornithine aminotransferase H537_RS0120050 H537_RS0137245

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