GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Synechococcus elongatus PCC 7942

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA

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 (21 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 Synpcc7942_0248 Synpcc7942_0247
AO353_03045 ABC transporter for L-Citrulline, permease component 2 Synpcc7942_0248
AO353_03040 ABC transporter for L-Citrulline, ATPase component Synpcc7942_0249 Synpcc7942_1680
citrullinase putative citrullinase Synpcc7942_2145
rocD ornithine aminotransferase Synpcc7942_0943 Synpcc7942_0645
rocA 1-pyrroline-5-carboxylate dehydrogenase
Alternative steps:
arcB ornithine carbamoyltransferase Synpcc7942_2514 Synpcc7942_0670
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase Synpcc7942_0943 Synpcc7942_0031
astD succinylglutamate semialdehyde dehydrogenase Synpcc7942_0489
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase
davD glutarate semialdehyde dehydrogenase
davT 5-aminovalerate aminotransferase Synpcc7942_0943 Synpcc7942_0645
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Synpcc7942_0597
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Synpcc7942_0684
gabD succinate semialdehyde dehydrogenase Synpcc7942_1857 Synpcc7942_0489
gabT gamma-aminobutyrate transaminase Synpcc7942_0943 Synpcc7942_0031
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
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) Synpcc7942_0943 Synpcc7942_0031
patD gamma-aminobutyraldehyde dehydrogenase Synpcc7942_0489
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 Synpcc7942_2058
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 Synpcc7942_0248
PS417_17605 ABC transporter for L-Citrulline, ATPase component Synpcc7942_0249 Synpcc7942_1680
puo putrescine oxidase Synpcc7942_0369
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase
puuA glutamate-putrescine ligase Synpcc7942_2296 Synpcc7942_2156
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Synpcc7942_0489
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 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