GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Acidovorax sp. GW101-3H11

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA

Also see fitness data for the top candidates

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component Ac3H11_2555
AO353_03050 ABC transporter for L-Citrulline, permease component 1 Ac3H11_2554 Ac3H11_3326
AO353_03045 ABC transporter for L-Citrulline, permease component 2 Ac3H11_3200 Ac3H11_3326
AO353_03040 ABC transporter for L-Citrulline, ATPase component Ac3H11_4899 Ac3H11_2553
citrullinase putative citrullinase Ac3H11_3030
ocd ornithine cyclodeaminase Ac3H11_4531
put1 proline dehydrogenase Ac3H11_2850
putA L-glutamate 5-semialdeyde dehydrogenase Ac3H11_2850 Ac3H11_3961
Alternative steps:
arcB ornithine carbamoyltransferase Ac3H11_1333 Ac3H11_3978
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase Ac3H11_1332 Ac3H11_4342
astD succinylglutamate semialdehyde dehydrogenase Ac3H11_3961 Ac3H11_1480
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Ac3H11_178 Ac3H11_2303
davD glutarate semialdehyde dehydrogenase Ac3H11_1480 Ac3H11_4184
davT 5-aminovalerate aminotransferase Ac3H11_4179 Ac3H11_1332
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Ac3H11_4006 Ac3H11_2775
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Ac3H11_1914 Ac3H11_4658
gabD succinate semialdehyde dehydrogenase Ac3H11_255 Ac3H11_1480
gabT gamma-aminobutyrate transaminase Ac3H11_4179 Ac3H11_4342
gcdG succinyl-CoA:glutarate CoA-transferase Ac3H11_3532 Ac3H11_198
gcdH glutaryl-CoA dehydrogenase Ac3H11_3533 Ac3H11_2991
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Ac3H11_4104
odc L-ornithine decarboxylase Ac3H11_2914
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) Ac3H11_4342 Ac3H11_1332
patD gamma-aminobutyraldehyde dehydrogenase Ac3H11_1496 Ac3H11_1486
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Ac3H11_4170
PRO3 pyrroline-5-carboxylate reductase Ac3H11_788
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component Ac3H11_2555
PS417_17595 ABC transporter for L-Citrulline, permease component 1 Ac3H11_3326 Ac3H11_2554
PS417_17600 ABC transporter for L-Citrulline, permease component 2 Ac3H11_3326 Ac3H11_4901
PS417_17605 ABC transporter for L-Citrulline, ATPase component Ac3H11_3200 Ac3H11_4899
puo putrescine oxidase
puuA glutamate-putrescine ligase Ac3H11_1551
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Ac3H11_1496 Ac3H11_1486
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Ac3H11_1167
rocA 1-pyrroline-5-carboxylate dehydrogenase Ac3H11_2850 Ac3H11_3961
rocD ornithine aminotransferase Ac3H11_4179 Ac3H11_1332

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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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