GapMind for catabolism of small carbon sources


L-citrulline catabolism in Chromobacterium vaccinii MWU205

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE


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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component VL52_RS17825 VL52_RS06115
AO353_03050 ABC transporter for L-Citrulline, permease component 1 VL52_RS17820 VL52_RS06120
AO353_03045 ABC transporter for L-Citrulline, permease component 2 VL52_RS17815 VL52_RS06125
AO353_03040 ABC transporter for L-Citrulline, ATPase component VL52_RS06130 VL52_RS19750
arcB ornithine carbamoyltransferase VL52_RS02435 VL52_RS21320
arcC carbamate kinase VL52_RS02430
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) VL52_RS15520 VL52_RS15515
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) VL52_RS15515 VL52_RS15520
astC succinylornithine transaminase VL52_RS15525 VL52_RS16645
astD succinylglutamate semialdehyde dehydrogenase VL52_RS15510 VL52_RS21455
astE succinylglutamate desuccinylase VL52_RS21985
Alternative steps:
atoB acetyl-CoA C-acetyltransferase VL52_RS14225 VL52_RS21005
citrullinase putative citrullinase VL52_RS09495
davD glutarate semialdehyde dehydrogenase VL52_RS20940 VL52_RS07105
davT 5-aminovalerate aminotransferase VL52_RS20935 VL52_RS15525
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase VL52_RS18865 VL52_RS21030
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase VL52_RS10360 VL52_RS21015
gabD succinate semialdehyde dehydrogenase VL52_RS20535 VL52_RS20940
gabT gamma-aminobutyrate transaminase VL52_RS20935 VL52_RS07075
gcdG succinyl-CoA:glutarate CoA-transferase VL52_RS20890
gcdH glutaryl-CoA dehydrogenase VL52_RS20895 VL52_RS19965
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) VL52_RS05540
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase VL52_RS08800 VL52_RS21315
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) VL52_RS07075 VL52_RS18210
patD gamma-aminobutyraldehyde dehydrogenase VL52_RS07105 VL52_RS21455
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase VL52_RS09515
PRO3 pyrroline-5-carboxylate reductase VL52_RS05330
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component VL52_RS06115 VL52_RS17825
PS417_17595 ABC transporter for L-Citrulline, permease component 1 VL52_RS06120 VL52_RS17820
PS417_17600 ABC transporter for L-Citrulline, permease component 2 VL52_RS06125 VL52_RS17815
PS417_17605 ABC transporter for L-Citrulline, ATPase component VL52_RS06130 VL52_RS19750
puo putrescine oxidase
put1 proline dehydrogenase VL52_RS18890
putA L-glutamate 5-semialdeyde dehydrogenase VL52_RS18890 VL52_RS20940
puuA glutamate-putrescine ligase VL52_RS07080 VL52_RS11885
puuB gamma-glutamylputrescine oxidase VL52_RS11115
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase VL52_RS07105 VL52_RS21455
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase VL52_RS07085
rocA 1-pyrroline-5-carboxylate dehydrogenase VL52_RS18890 VL52_RS20940
rocD ornithine aminotransferase VL52_RS15525 VL52_RS20935

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