GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Erythrobacter marinus HWDM-33

Best path

PS417_17590, PS417_17595, PS417_17600, PS417_17605, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
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 AAV99_RS11970 AAV99_RS13340
citrullinase putative citrullinase AAV99_RS05660
ocd ornithine cyclodeaminase
put1 proline dehydrogenase AAV99_RS05475
putA L-glutamate 5-semialdeyde dehydrogenase AAV99_RS05475 AAV99_RS05570
Alternative steps:
AO353_03040 ABC transporter for L-Citrulline, ATPase component AAV99_RS11970 AAV99_RS13340
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03050 ABC transporter for L-Citrulline, permease component 1
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component
arcB ornithine carbamoyltransferase AAV99_RS04905 AAV99_RS01325
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) AAV99_RS11705
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) AAV99_RS11705
astC succinylornithine transaminase AAV99_RS04900 AAV99_RS12000
astD succinylglutamate semialdehyde dehydrogenase AAV99_RS06745 AAV99_RS05570
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase AAV99_RS12435 AAV99_RS09865
davD glutarate semialdehyde dehydrogenase AAV99_RS05570 AAV99_RS10950
davT 5-aminovalerate aminotransferase AAV99_RS04900 AAV99_RS12000
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AAV99_RS05725 AAV99_RS12275
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AAV99_RS07705 AAV99_RS00990
gabD succinate semialdehyde dehydrogenase AAV99_RS05570 AAV99_RS05185
gabT gamma-aminobutyrate transaminase AAV99_RS04900 AAV99_RS12000
gcdG succinyl-CoA:glutarate CoA-transferase AAV99_RS11935 AAV99_RS02665
gcdH glutaryl-CoA dehydrogenase AAV99_RS06380 AAV99_RS03120
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
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) AAV99_RS04900 AAV99_RS12000
patD gamma-aminobutyraldehyde dehydrogenase AAV99_RS05570 AAV99_RS05185
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 AAV99_RS00615
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AAV99_RS05570 AAV99_RS05730
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase AAV99_RS05475 AAV99_RS05570
rocD ornithine aminotransferase AAV99_RS04900 AAV99_RS12000

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