GapMind for catabolism of small carbon sources


L-citrulline catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, ocd, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component CEV31_RS14700 CEV31_RS14695
PS417_17595 ABC transporter for L-Citrulline, permease component 1 CEV31_RS11195 CEV31_RS20085
PS417_17600 ABC transporter for L-Citrulline, permease component 2 CEV31_RS11190 CEV31_RS20080
PS417_17605 ABC transporter for L-Citrulline, ATPase component CEV31_RS19205 CEV31_RS20075
citrullinase putative citrullinase CEV31_RS19180
ocd ornithine cyclodeaminase CEV31_RS02450
put1 proline dehydrogenase CEV31_RS15250 CEV31_RS01735
putA L-glutamate 5-semialdeyde dehydrogenase CEV31_RS15250 CEV31_RS01730
Alternative steps:
AO353_03040 ABC transporter for L-Citrulline, ATPase component CEV31_RS20075 CEV31_RS19205
AO353_03045 ABC transporter for L-Citrulline, permease component 2 CEV31_RS20080 CEV31_RS19200
AO353_03050 ABC transporter for L-Citrulline, permease component 1 CEV31_RS11195 CEV31_RS20085
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component CEV31_RS11200 CEV31_RS14700
arcB ornithine carbamoyltransferase CEV31_RS07280 CEV31_RS16395
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase CEV31_RS07275 CEV31_RS17075
astD succinylglutamate semialdehyde dehydrogenase CEV31_RS17495 CEV31_RS18595
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase CEV31_RS03605 CEV31_RS02650
davD glutarate semialdehyde dehydrogenase CEV31_RS02995 CEV31_RS17495
davT 5-aminovalerate aminotransferase CEV31_RS07275 CEV31_RS17075
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CEV31_RS05620 CEV31_RS09090
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CEV31_RS15760 CEV31_RS04315
gabD succinate semialdehyde dehydrogenase CEV31_RS02995 CEV31_RS17935
gabT gamma-aminobutyrate transaminase CEV31_RS17470 CEV31_RS19110
gcdG succinyl-CoA:glutarate CoA-transferase CEV31_RS11730 CEV31_RS09080
gcdH glutaryl-CoA dehydrogenase CEV31_RS11735 CEV31_RS05790
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) CEV31_RS17795 CEV31_RS18945
odc L-ornithine decarboxylase CEV31_RS13805
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) CEV31_RS19110 CEV31_RS17470
patD gamma-aminobutyraldehyde dehydrogenase CEV31_RS19025 CEV31_RS08350
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase CEV31_RS03690
PRO3 pyrroline-5-carboxylate reductase CEV31_RS15700
puo putrescine oxidase
puuA glutamate-putrescine ligase CEV31_RS15610 CEV31_RS09105
puuB gamma-glutamylputrescine oxidase CEV31_RS15615 CEV31_RS19040
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase CEV31_RS06610 CEV31_RS16975
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase CEV31_RS02805
rocA 1-pyrroline-5-carboxylate dehydrogenase CEV31_RS15250 CEV31_RS01730
rocD ornithine aminotransferase CEV31_RS17075 CEV31_RS17470

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