GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Mesorhizobium ciceri WSM1271

Best path

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

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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component Mesci_3923 Mesci_0696
AO353_03050 ABC transporter for L-Citrulline, permease component 1 Mesci_0319 Mesci_5618
AO353_03045 ABC transporter for L-Citrulline, permease component 2 Mesci_2592 Mesci_0320
AO353_03040 ABC transporter for L-Citrulline, ATPase component Mesci_0317 Mesci_2595
citrullinase putative citrullinase Mesci_5622
ocd ornithine cyclodeaminase Mesci_5621 Mesci_2494
put1 proline dehydrogenase Mesci_3431
putA L-glutamate 5-semialdeyde dehydrogenase Mesci_3431 Mesci_0274
Alternative steps:
arcB ornithine carbamoyltransferase Mesci_5986 Mesci_4015
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase Mesci_5987 Mesci_0044
astD succinylglutamate semialdehyde dehydrogenase Mesci_5665 Mesci_4924
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Mesci_1329 Mesci_1095
davD glutarate semialdehyde dehydrogenase Mesci_3425 Mesci_5665
davT 5-aminovalerate aminotransferase Mesci_0044 Mesci_5987
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Mesci_6037 Mesci_4665
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Mesci_1071 Mesci_6001
gabD succinate semialdehyde dehydrogenase Mesci_5665 Mesci_5386
gabT gamma-aminobutyrate transaminase Mesci_0044 Mesci_3398
gcdG succinyl-CoA:glutarate CoA-transferase Mesci_3113 Mesci_0263
gcdH glutaryl-CoA dehydrogenase Mesci_1983 Mesci_4845
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Mesci_2427
odc L-ornithine decarboxylase Mesci_1913
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 Mesci_5949
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) Mesci_3398 Mesci_5677
patD gamma-aminobutyraldehyde dehydrogenase Mesci_0148 Mesci_4924
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase Mesci_1233 Mesci_0177
PRO3 pyrroline-5-carboxylate reductase Mesci_2392
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component Mesci_5980 Mesci_0318
PS417_17595 ABC transporter for L-Citrulline, permease component 1 Mesci_5618 Mesci_0319
PS417_17600 ABC transporter for L-Citrulline, permease component 2 Mesci_2592 Mesci_3925
PS417_17605 ABC transporter for L-Citrulline, ATPase component Mesci_2595 Mesci_0317
puo putrescine oxidase
puuA glutamate-putrescine ligase Mesci_2412 Mesci_1090
puuB gamma-glutamylputrescine oxidase Mesci_1091 Mesci_2410
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Mesci_2633 Mesci_0690
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Mesci_0345
rocA 1-pyrroline-5-carboxylate dehydrogenase Mesci_3431 Mesci_0274
rocD ornithine aminotransferase Mesci_0044 Mesci_5288

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