GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Flavobacterium ummariense DS-12

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 (22 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 BM253_RS02520 BM253_RS12820
citrullinase putative citrullinase BM253_RS08205
rocD ornithine aminotransferase BM253_RS04065 BM253_RS04610
rocA 1-pyrroline-5-carboxylate dehydrogenase BM253_RS09455 BM253_RS15450
Alternative steps:
arcB ornithine carbamoyltransferase BM253_RS14640
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase BM253_RS04065 BM253_RS04610
astD succinylglutamate semialdehyde dehydrogenase BM253_RS02660 BM253_RS15450
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase BM253_RS12775 BM253_RS15640
davD glutarate semialdehyde dehydrogenase BM253_RS15450 BM253_RS02725
davT 5-aminovalerate aminotransferase BM253_RS04610 BM253_RS04065
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BM253_RS01100 BM253_RS15650
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BM253_RS15650 BM253_RS03300
gabD succinate semialdehyde dehydrogenase BM253_RS02725 BM253_RS15450
gabT gamma-aminobutyrate transaminase BM253_RS04610 BM253_RS08990
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase BM253_RS00785 BM253_RS12625
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 BM253_RS00405
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) BM253_RS04610 BM253_RS04065
patD gamma-aminobutyraldehyde dehydrogenase BM253_RS15450 BM253_RS02660
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
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 BM253_RS02520 BM253_RS04260
puo putrescine oxidase
put1 proline dehydrogenase BM253_RS14675
putA L-glutamate 5-semialdeyde dehydrogenase BM253_RS09455 BM253_RS15450
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BM253_RS15450
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 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