GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Marinobacter guineae M3B

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component CLH62_RS07715 CLH62_RS11920
AO353_03050 ABC transporter for L-Citrulline, permease component 1 CLH62_RS07720 CLH62_RS06595
AO353_03045 ABC transporter for L-Citrulline, permease component 2 CLH62_RS07725 CLH62_RS11905
AO353_03040 ABC transporter for L-Citrulline, ATPase component CLH62_RS07710 CLH62_RS11910
arcB ornithine carbamoyltransferase CLH62_RS09965 CLH62_RS16745
arcC carbamate kinase CLH62_RS09960
odc L-ornithine decarboxylase CLH62_RS11085
puuA glutamate-putrescine ligase CLH62_RS15815 CLH62_RS14055
puuB gamma-glutamylputrescine oxidase CLH62_RS15805
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase CLH62_RS15810 CLH62_RS14090
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase CLH62_RS03735
gabT gamma-aminobutyrate transaminase CLH62_RS11925 CLH62_RS11500
gabD succinate semialdehyde dehydrogenase CLH62_RS09265 CLH62_RS11930
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) CLH62_RS07765 CLH62_RS07760
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) CLH62_RS07760 CLH62_RS07765
astC succinylornithine transaminase CLH62_RS07770 CLH62_RS11880
astD succinylglutamate semialdehyde dehydrogenase CLH62_RS07755 CLH62_RS10190
astE succinylglutamate desuccinylase CLH62_RS07730
atoB acetyl-CoA C-acetyltransferase CLH62_RS07455 CLH62_RS15420
citrullinase putative citrullinase CLH62_RS02325
davD glutarate semialdehyde dehydrogenase CLH62_RS09265 CLH62_RS11930
davT 5-aminovalerate aminotransferase CLH62_RS11925 CLH62_RS11500
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CLH62_RS15970 CLH62_RS10205
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CLH62_RS18530 CLH62_RS10205
gcdG succinyl-CoA:glutarate CoA-transferase CLH62_RS09260 CLH62_RS14995
gcdH glutaryl-CoA dehydrogenase CLH62_RS10225 CLH62_RS15440
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase CLH62_RS12060
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) CLH62_RS15685 CLH62_RS06625
patD gamma-aminobutyraldehyde dehydrogenase CLH62_RS01385 CLH62_RS15810
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 CLH62_RS08390
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component CLH62_RS07715 CLH62_RS11920
PS417_17595 ABC transporter for L-Citrulline, permease component 1 CLH62_RS07720 CLH62_RS11905
PS417_17600 ABC transporter for L-Citrulline, permease component 2 CLH62_RS07725 CLH62_RS07720
PS417_17605 ABC transporter for L-Citrulline, ATPase component CLH62_RS07710 CLH62_RS11910
puo putrescine oxidase
put1 proline dehydrogenase CLH62_RS05435
putA L-glutamate 5-semialdeyde dehydrogenase CLH62_RS05435 CLH62_RS11815
rocA 1-pyrroline-5-carboxylate dehydrogenase CLH62_RS05435 CLH62_RS11815
rocD ornithine aminotransferase CLH62_RS11500 CLH62_RS11925

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