GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Halioglobus japonicus S1-36

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 (27 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 C0029_RS05165 C0029_RS10470
citrullinase putative citrullinase C0029_RS11700
rocD ornithine aminotransferase C0029_RS18740 C0029_RS13280
PRO3 pyrroline-5-carboxylate reductase C0029_RS11970
put1 proline dehydrogenase C0029_RS02865
putA L-glutamate 5-semialdeyde dehydrogenase C0029_RS02865 C0029_RS01835
Alternative steps:
arcB ornithine carbamoyltransferase C0029_RS18735 C0029_RS14740
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase C0029_RS18740 C0029_RS09770
astD succinylglutamate semialdehyde dehydrogenase C0029_RS09070 C0029_RS01440
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase C0029_RS06075 C0029_RS04970
davD glutarate semialdehyde dehydrogenase C0029_RS01440 C0029_RS01835
davT 5-aminovalerate aminotransferase C0029_RS18740 C0029_RS09770
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase C0029_RS04910 C0029_RS05670
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase C0029_RS18685 C0029_RS02360
gabD succinate semialdehyde dehydrogenase C0029_RS01440 C0029_RS01835
gabT gamma-aminobutyrate transaminase C0029_RS03250 C0029_RS09790
gcdG succinyl-CoA:glutarate CoA-transferase C0029_RS13315 C0029_RS04725
gcdH glutaryl-CoA dehydrogenase C0029_RS13310 C0029_RS16975
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 C0029_RS04290
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) C0029_RS13280 C0029_RS03250
patD gamma-aminobutyraldehyde dehydrogenase C0029_RS01835 C0029_RS09070
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC C0029_RS00070
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 C0029_RS05165 C0029_RS11915
puo putrescine oxidase
puuA glutamate-putrescine ligase C0029_RS16465 C0029_RS13285
puuB gamma-glutamylputrescine oxidase C0029_RS01760 C0029_RS09780
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase C0029_RS01835 C0029_RS01440
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase C0029_RS02865 C0029_RS01835

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 Sep 24 2021. 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