GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Magnetospirillum magneticum AMB-1

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, 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 (25 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 AMB_RS10565 AMB_RS06945
arcB ornithine carbamoyltransferase AMB_RS01610 AMB_RS18300
arcC carbamate kinase
rocD ornithine aminotransferase AMB_RS04150 AMB_RS08515
PRO3 pyrroline-5-carboxylate reductase AMB_RS02820
put1 proline dehydrogenase AMB_RS12610
putA L-glutamate 5-semialdeyde dehydrogenase AMB_RS12610 AMB_RS04115
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase AMB_RS01605 AMB_RS04150
astD succinylglutamate semialdehyde dehydrogenase AMB_RS06710 AMB_RS04115
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase AMB_RS18210 AMB_RS04295
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase AMB_RS06710 AMB_RS04160
davT 5-aminovalerate aminotransferase AMB_RS01605 AMB_RS04150
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AMB_RS03265 AMB_RS13070
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AMB_RS15050 AMB_RS19750
gabD succinate semialdehyde dehydrogenase AMB_RS06710 AMB_RS04160
gabT gamma-aminobutyrate transaminase AMB_RS08515 AMB_RS01605
gcdG succinyl-CoA:glutarate CoA-transferase AMB_RS08365 AMB_RS07510
gcdH glutaryl-CoA dehydrogenase AMB_RS16315 AMB_RS03480
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) AMB_RS19325
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase AMB_RS05630 AMB_RS07020
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) AMB_RS08515 AMB_RS04150
patD gamma-aminobutyraldehyde dehydrogenase AMB_RS06710 AMB_RS04115
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
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 AMB_RS10565 AMB_RS06945
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AMB_RS04115 AMB_RS06710
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase AMB_RS20870
rocA 1-pyrroline-5-carboxylate dehydrogenase AMB_RS12610 AMB_RS04115

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.

Links

Downloads

Related tools

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, 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