GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Cereibacter sphaeroides ATCC 17029

Best path

PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD

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 (33 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 RSPH17029_RS17505 RSPH17029_RS15650
PS417_17600 ABC transporter for L-Citrulline, permease component 2 RSPH17029_RS10180 RSPH17029_RS17505
PS417_17605 ABC transporter for L-Citrulline, ATPase component RSPH17029_RS10165 RSPH17029_RS17510
arcB ornithine carbamoyltransferase RSPH17029_RS03670 RSPH17029_RS13430
arcC carbamate kinase
odc L-ornithine decarboxylase RSPH17029_RS03580
puuA glutamate-putrescine ligase RSPH17029_RS10230 RSPH17029_RS01120
puuB gamma-glutamylputrescine oxidase RSPH17029_RS10235 RSPH17029_RS11565
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase RSPH17029_RS16005 RSPH17029_RS04350
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase RSPH17029_RS09530 RSPH17029_RS03635
gabT gamma-aminobutyrate transaminase RSPH17029_RS04315 RSPH17029_RS20165
gabD succinate semialdehyde dehydrogenase RSPH17029_RS13480 RSPH17029_RS16005
Alternative steps:
AO353_03040 ABC transporter for L-Citrulline, ATPase component RSPH17029_RS10165 RSPH17029_RS17510
AO353_03045 ABC transporter for L-Citrulline, permease component 2 RSPH17029_RS17505 RSPH17029_RS10180
AO353_03050 ABC transporter for L-Citrulline, permease component 1 RSPH17029_RS17505 RSPH17029_RS10175
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component RSPH17029_RS10170
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase RSPH17029_RS03665 RSPH17029_RS04315
astD succinylglutamate semialdehyde dehydrogenase RSPH17029_RS13480 RSPH17029_RS16005
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase RSPH17029_RS12120 RSPH17029_RS19805
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase RSPH17029_RS13480 RSPH17029_RS04350
davT 5-aminovalerate aminotransferase RSPH17029_RS04315 RSPH17029_RS17535
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RSPH17029_RS00050 RSPH17029_RS17990
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RSPH17029_RS16015 RSPH17029_RS04435
gcdG succinyl-CoA:glutarate CoA-transferase RSPH17029_RS00595
gcdH glutaryl-CoA dehydrogenase RSPH17029_RS14905 RSPH17029_RS05935
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) RSPH17029_RS10685
ocd ornithine cyclodeaminase
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) RSPH17029_RS20165 RSPH17029_RS16010
patD gamma-aminobutyraldehyde dehydrogenase RSPH17029_RS16005 RSPH17029_RS04350
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase RSPH17029_RS15945
PRO3 pyrroline-5-carboxylate reductase RSPH17029_RS15160
puo putrescine oxidase
put1 proline dehydrogenase RSPH17029_RS04265 RSPH17029_RS07235
putA L-glutamate 5-semialdeyde dehydrogenase RSPH17029_RS04265 RSPH17029_RS16005
rocA 1-pyrroline-5-carboxylate dehydrogenase RSPH17029_RS04265 RSPH17029_RS16005
rocD ornithine aminotransferase RSPH17029_RS04315 RSPH17029_RS20165

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 Apr 10 2024. 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