GapMind for catabolism of small carbon sources


L-citrulline catabolism in Photobacterium jeanii R-40508

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA


Overview: Citrulline can be catabolized via ornithine carbamoyltransferase in reverse (PMID:3129535). Genetic evidence suggests that some bacteria use a putative citrullinase (EC to consume citrulline.

51 steps (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component A3K86_RS13005 A3K86_RS01795
AO353_03050 ABC transporter for L-Citrulline, permease component 1 A3K86_RS13010 A3K86_RS01790
AO353_03045 ABC transporter for L-Citrulline, permease component 2 A3K86_RS13015 A3K86_RS01785
AO353_03040 ABC transporter for L-Citrulline, ATPase component A3K86_RS13000 A3K86_RS01690
arcB ornithine carbamoyltransferase A3K86_RS01390 A3K86_RS18210
arcC carbamate kinase A3K86_RS18220 A3K86_RS01395
rocD ornithine aminotransferase A3K86_RS14790 A3K86_RS04565
PRO3 pyrroline-5-carboxylate reductase A3K86_RS00145
put1 proline dehydrogenase A3K86_RS18285
putA L-glutamate 5-semialdeyde dehydrogenase A3K86_RS18285 A3K86_RS19720
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) A3K86_RS09060
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) A3K86_RS09060
astC succinylornithine transaminase A3K86_RS09055 A3K86_RS14790
astD succinylglutamate semialdehyde dehydrogenase A3K86_RS09065 A3K86_RS19720
astE succinylglutamate desuccinylase A3K86_RS04085
atoB acetyl-CoA C-acetyltransferase A3K86_RS19875 A3K86_RS15935
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase A3K86_RS14375 A3K86_RS19720
davT 5-aminovalerate aminotransferase A3K86_RS09055 A3K86_RS14790
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase A3K86_RS15920 A3K86_RS17390
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase A3K86_RS17390 A3K86_RS06710
gabD succinate semialdehyde dehydrogenase A3K86_RS14375 A3K86_RS19720
gabT gamma-aminobutyrate transaminase A3K86_RS09055 A3K86_RS14790
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase A3K86_RS15945 A3K86_RS15925
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 A3K86_RS13045
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) A3K86_RS09055 A3K86_RS14790
patD gamma-aminobutyraldehyde dehydrogenase A3K86_RS19720 A3K86_RS14375
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 A3K86_RS13005
PS417_17595 ABC transporter for L-Citrulline, permease component 1 A3K86_RS13010 A3K86_RS01790
PS417_17600 ABC transporter for L-Citrulline, permease component 2 A3K86_RS13015 A3K86_RS01785
PS417_17605 ABC transporter for L-Citrulline, ATPase component A3K86_RS13000 A3K86_RS21200
puo putrescine oxidase
puuA glutamate-putrescine ligase A3K86_RS00765
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase A3K86_RS19720 A3K86_RS14375
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase A3K86_RS18285 A3K86_RS19720

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