GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Nocardioides dokdonensis FR1436

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 (29 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 I601_RS08985
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component I601_RS07015 I601_RS08990
arcB ornithine carbamoyltransferase I601_RS14610 I601_RS15160
arcC carbamate kinase I601_RS14605 I601_RS06530
rocD ornithine aminotransferase I601_RS01940 I601_RS14155
PRO3 pyrroline-5-carboxylate reductase I601_RS04100
put1 proline dehydrogenase I601_RS04105 I601_RS05875
putA L-glutamate 5-semialdeyde dehydrogenase I601_RS10820 I601_RS01590
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase I601_RS15155 I601_RS01940
astD succinylglutamate semialdehyde dehydrogenase I601_RS01590 I601_RS01130
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase I601_RS03035 I601_RS19250
citrullinase putative citrullinase I601_RS13900
davD glutarate semialdehyde dehydrogenase I601_RS05735 I601_RS14160
davT 5-aminovalerate aminotransferase I601_RS14155 I601_RS12790
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase I601_RS19165 I601_RS05525
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase I601_RS04220 I601_RS05790
gabD succinate semialdehyde dehydrogenase I601_RS05735 I601_RS01585
gabT gamma-aminobutyrate transaminase I601_RS14155 I601_RS12790
gcdG succinyl-CoA:glutarate CoA-transferase I601_RS06545 I601_RS10415
gcdH glutaryl-CoA dehydrogenase I601_RS02110 I601_RS10230
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) I601_RS15155 I601_RS12765
patD gamma-aminobutyraldehyde dehydrogenase I601_RS12775 I601_RS01380
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 I601_RS07010
PS417_17600 ABC transporter for L-Citrulline, permease component 2 I601_RS07010
PS417_17605 ABC transporter for L-Citrulline, ATPase component I601_RS07015 I601_RS08990
puo putrescine oxidase I601_RS02660
puuA glutamate-putrescine ligase I601_RS13805 I601_RS14195
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase I601_RS01130 I601_RS01590
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase I601_RS10820 I601_RS01590

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