GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Erythrobacter gangjinensis K7-2

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, 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 (26 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 AAW01_RS09690 AAW01_RS11525
citrullinase putative citrullinase AAW01_RS09855
ocd ornithine cyclodeaminase
put1 proline dehydrogenase AAW01_RS11260
putA L-glutamate 5-semialdeyde dehydrogenase AAW01_RS11260 AAW01_RS09770
Alternative steps:
arcB ornithine carbamoyltransferase AAW01_RS09060 AAW01_RS06590
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) AAW01_RS05075
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) AAW01_RS05075
astC succinylornithine transaminase AAW01_RS09055
astD succinylglutamate semialdehyde dehydrogenase AAW01_RS11975 AAW01_RS11260
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase AAW01_RS02970 AAW01_RS00830
davD glutarate semialdehyde dehydrogenase AAW01_RS09770 AAW01_RS04300
davT 5-aminovalerate aminotransferase AAW01_RS09055 AAW01_RS12605
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AAW01_RS13205 AAW01_RS11465
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AAW01_RS00825 AAW01_RS06205
gabD succinate semialdehyde dehydrogenase AAW01_RS09770 AAW01_RS04390
gabT gamma-aminobutyrate transaminase AAW01_RS09055 AAW01_RS12605
gcdG succinyl-CoA:glutarate CoA-transferase AAW01_RS11415 AAW01_RS11420
gcdH glutaryl-CoA dehydrogenase AAW01_RS11555 AAW01_RS07145
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) AAW01_RS09055 AAW01_RS12605
patD gamma-aminobutyraldehyde dehydrogenase AAW01_RS09770 AAW01_RS04390
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 AAW01_RS05825
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 AAW01_RS07155 AAW01_RS09690
puo putrescine oxidase
puuA glutamate-putrescine ligase AAW01_RS06010
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AAW01_RS09770 AAW01_RS13220
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase AAW01_RS11260 AAW01_RS09770
rocD ornithine aminotransferase AAW01_RS12605 AAW01_RS09055

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