GapMind for catabolism of small carbon sources


L-citrulline catabolism in Burkholderia phytofirmans PsJN

Best path

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

Also see fitness data for the top candidates


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 BPHYT_RS29525 BPHYT_RS07735
AO353_03050 ABC transporter for L-Citrulline, permease component 1 BPHYT_RS05505 BPHYT_RS07675
AO353_03045 ABC transporter for L-Citrulline, permease component 2 BPHYT_RS07680 BPHYT_RS05500
AO353_03040 ABC transporter for L-Citrulline, ATPase component BPHYT_RS05495 BPHYT_RS07685
arcB ornithine carbamoyltransferase BPHYT_RS27685 BPHYT_RS15915
arcC carbamate kinase BPHYT_RS27690
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) BPHYT_RS07700 BPHYT_RS07705
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) BPHYT_RS07705 BPHYT_RS07700
astC succinylornithine transaminase BPHYT_RS07695 BPHYT_RS15580
astD succinylglutamate semialdehyde dehydrogenase BPHYT_RS07710 BPHYT_RS25810
astE succinylglutamate desuccinylase BPHYT_RS07720
Alternative steps:
atoB acetyl-CoA C-acetyltransferase BPHYT_RS09150 BPHYT_RS09180
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase BPHYT_RS22430 BPHYT_RS34305
davT 5-aminovalerate aminotransferase BPHYT_RS22435 BPHYT_RS07695
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BPHYT_RS17335 BPHYT_RS28020
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BPHYT_RS13545 BPHYT_RS03225
gabD succinate semialdehyde dehydrogenase BPHYT_RS10925 BPHYT_RS34305
gabT gamma-aminobutyrate transaminase BPHYT_RS23155 BPHYT_RS22435
gcdG succinyl-CoA:glutarate CoA-transferase BPHYT_RS13985 BPHYT_RS31850
gcdH glutaryl-CoA dehydrogenase BPHYT_RS03780 BPHYT_RS23260
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BPHYT_RS28480 BPHYT_RS01855
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase BPHYT_RS04980 BPHYT_RS00645
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) BPHYT_RS23155 BPHYT_RS30220
patD gamma-aminobutyraldehyde dehydrogenase BPHYT_RS23175 BPHYT_RS25160
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase BPHYT_RS28265 BPHYT_RS22640
PRO3 pyrroline-5-carboxylate reductase BPHYT_RS03490
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component BPHYT_RS29525 BPHYT_RS10140
PS417_17595 ABC transporter for L-Citrulline, permease component 1 BPHYT_RS05505 BPHYT_RS07675
PS417_17600 ABC transporter for L-Citrulline, permease component 2 BPHYT_RS05500 BPHYT_RS07680
PS417_17605 ABC transporter for L-Citrulline, ATPase component BPHYT_RS07685 BPHYT_RS05495
puo putrescine oxidase BPHYT_RS09910
put1 proline dehydrogenase BPHYT_RS19355 BPHYT_RS29290
putA L-glutamate 5-semialdeyde dehydrogenase BPHYT_RS19355 BPHYT_RS28770
puuA glutamate-putrescine ligase BPHYT_RS23160 BPHYT_RS09955
puuB gamma-glutamylputrescine oxidase BPHYT_RS23125 BPHYT_RS23120
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BPHYT_RS23175 BPHYT_RS29875
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase BPHYT_RS23165 BPHYT_RS15045
rocA 1-pyrroline-5-carboxylate dehydrogenase BPHYT_RS19355 BPHYT_RS28770
rocD ornithine aminotransferase BPHYT_RS22435 BPHYT_RS10155

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 17 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