GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Novosphingobium aromaticivorans DSM 12444

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, 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 (27 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 SARO_RS05745 SARO_RS11475
citrullinase putative citrullinase SARO_RS15710
rocD ornithine aminotransferase SARO_RS13120 SARO_RS14875
PRO3 pyrroline-5-carboxylate reductase SARO_RS05695
put1 proline dehydrogenase SARO_RS03520 SARO_RS14900
putA L-glutamate 5-semialdeyde dehydrogenase SARO_RS03520 SARO_RS14550
Alternative steps:
arcB ornithine carbamoyltransferase SARO_RS15950 SARO_RS15545
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) SARO_RS04420
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) SARO_RS04420
astC succinylornithine transaminase SARO_RS15955 SARO_RS13120
astD succinylglutamate semialdehyde dehydrogenase SARO_RS04690 SARO_RS17080
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase SARO_RS04040 SARO_RS05335
davD glutarate semialdehyde dehydrogenase SARO_RS17165 SARO_RS14885
davT 5-aminovalerate aminotransferase SARO_RS13120 SARO_RS15955
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SARO_RS04305 SARO_RS07105
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SARO_RS02760 SARO_RS18115
gabD succinate semialdehyde dehydrogenase SARO_RS13125 SARO_RS03980
gabT gamma-aminobutyrate transaminase SARO_RS14875 SARO_RS13120
gcdG succinyl-CoA:glutarate CoA-transferase SARO_RS18980 SARO_RS17240
gcdH glutaryl-CoA dehydrogenase SARO_RS17970 SARO_RS08250
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) SARO_RS14875 SARO_RS15955
patD gamma-aminobutyraldehyde dehydrogenase SARO_RS14550 SARO_RS19930
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 SARO_RS11475 SARO_RS14425
puo putrescine oxidase
puuA glutamate-putrescine ligase SARO_RS13155
puuB gamma-glutamylputrescine oxidase SARO_RS14935 SARO_RS01270
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase SARO_RS14895 SARO_RS14550
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase SARO_RS03520 SARO_RS14550

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 09 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