GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Geobacter daltonii FRC-32

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, 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 (24 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 GEOB_RS03640 GEOB_RS10430
arcB ornithine carbamoyltransferase GEOB_RS05590 GEOB_RS16210
arcC carbamate kinase
rocD ornithine aminotransferase GEOB_RS05585 GEOB_RS14935
rocA 1-pyrroline-5-carboxylate dehydrogenase GEOB_RS12935 GEOB_RS17645
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase GEOB_RS05585 GEOB_RS14935
astD succinylglutamate semialdehyde dehydrogenase GEOB_RS12935 GEOB_RS17645
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase GEOB_RS01200 GEOB_RS00490
citrullinase putative citrullinase GEOB_RS11655
davD glutarate semialdehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
davT 5-aminovalerate aminotransferase GEOB_RS05585 GEOB_RS14935
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase GEOB_RS00800 GEOB_RS01210
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase GEOB_RS00795 GEOB_RS00835
gabD succinate semialdehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
gabT gamma-aminobutyrate transaminase GEOB_RS14935 GEOB_RS02285
gcdG succinyl-CoA:glutarate CoA-transferase GEOB_RS12030
gcdH glutaryl-CoA dehydrogenase GEOB_RS10880 GEOB_RS01170
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
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) GEOB_RS14935 GEOB_RS05585
patD gamma-aminobutyraldehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
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 GEOB_RS08330
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 GEOB_RS10490 GEOB_RS08235
puo putrescine oxidase
put1 proline dehydrogenase GEOB_RS12935
putA L-glutamate 5-semialdeyde dehydrogenase GEOB_RS12935 GEOB_RS17645
puuA glutamate-putrescine ligase GEOB_RS14845
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
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