GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, 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 (26 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 Echvi_2204 Echvi_4044
citrullinase putative citrullinase Echvi_0366
rocD ornithine aminotransferase Echvi_0577 Echvi_2919
PRO3 pyrroline-5-carboxylate reductase Echvi_2635 Echvi_2479
put1 proline dehydrogenase Echvi_0119
putA L-glutamate 5-semialdeyde dehydrogenase Echvi_1300 Echvi_0481
Alternative steps:
arcB ornithine carbamoyltransferase Echvi_4661 Echvi_3849
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase Echvi_3848 Echvi_0577
astD succinylglutamate semialdehyde dehydrogenase Echvi_0481
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Echvi_3705 Echvi_1071
davD glutarate semialdehyde dehydrogenase Echvi_0481 Echvi_3822
davT 5-aminovalerate aminotransferase Echvi_2919 Echvi_3848
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Echvi_4069 Echvi_0069
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Echvi_1069 Echvi_3304
gabD succinate semialdehyde dehydrogenase Echvi_3822 Echvi_0481
gabT gamma-aminobutyrate transaminase Echvi_2919 Echvi_2790
gcdG succinyl-CoA:glutarate CoA-transferase Echvi_1686 Echvi_1687
gcdH glutaryl-CoA dehydrogenase Echvi_2990 Echvi_0738
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Echvi_3348
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 Echvi_2799
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) Echvi_2919 Echvi_0577
patD gamma-aminobutyraldehyde dehydrogenase Echvi_0481 Echvi_3822
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Echvi_3951
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 Echvi_4044 Echvi_2909
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Echvi_0481 Echvi_3822
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase Echvi_1300 Echvi_0481

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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