GapMind for catabolism of small carbon sources


L-citrulline catabolism in Paraburkholderia bryophila 376MFSha3.1

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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component H281DRAFT_01522 H281DRAFT_00224
AO353_03050 ABC transporter for L-Citrulline, permease component 1 H281DRAFT_00223 H281DRAFT_06474
AO353_03045 ABC transporter for L-Citrulline, permease component 2 H281DRAFT_06475 H281DRAFT_00222
AO353_03040 ABC transporter for L-Citrulline, ATPase component H281DRAFT_06476 H281DRAFT_00221
arcB ornithine carbamoyltransferase H281DRAFT_04119 H281DRAFT_01493
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) H281DRAFT_06479 H281DRAFT_06480
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) H281DRAFT_06480 H281DRAFT_06479
astC succinylornithine transaminase H281DRAFT_06478 H281DRAFT_04057
astD succinylglutamate semialdehyde dehydrogenase H281DRAFT_06481 H281DRAFT_00213
astE succinylglutamate desuccinylase H281DRAFT_06483
Alternative steps:
atoB acetyl-CoA C-acetyltransferase H281DRAFT_00852 H281DRAFT_00857
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase H281DRAFT_03178 H281DRAFT_03540
davT 5-aminovalerate aminotransferase H281DRAFT_03179 H281DRAFT_06478
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H281DRAFT_05725 H281DRAFT_02514
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H281DRAFT_00361 H281DRAFT_04625
gabD succinate semialdehyde dehydrogenase H281DRAFT_01155 H281DRAFT_03540
gabT gamma-aminobutyrate transaminase H281DRAFT_01082 H281DRAFT_03179
gcdG succinyl-CoA:glutarate CoA-transferase H281DRAFT_04444 H281DRAFT_01169
gcdH glutaryl-CoA dehydrogenase H281DRAFT_04737 H281DRAFT_01204
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H281DRAFT_02167
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase H281DRAFT_00160
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) H281DRAFT_01082 H281DRAFT_06342
patD gamma-aminobutyraldehyde dehydrogenase H281DRAFT_02464 H281DRAFT_00993
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase H281DRAFT_01193
PRO3 pyrroline-5-carboxylate reductase H281DRAFT_04679
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component H281DRAFT_01522 H281DRAFT_00224
PS417_17595 ABC transporter for L-Citrulline, permease component 1 H281DRAFT_00223 H281DRAFT_06474
PS417_17600 ABC transporter for L-Citrulline, permease component 2 H281DRAFT_00222 H281DRAFT_06475
PS417_17605 ABC transporter for L-Citrulline, ATPase component H281DRAFT_06476 H281DRAFT_00221
puo putrescine oxidase
put1 proline dehydrogenase H281DRAFT_02404 H281DRAFT_06542
putA L-glutamate 5-semialdeyde dehydrogenase H281DRAFT_02404 H281DRAFT_03016
puuA glutamate-putrescine ligase H281DRAFT_01081 H281DRAFT_00452
puuB gamma-glutamylputrescine oxidase H281DRAFT_03219 H281DRAFT_06337
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase H281DRAFT_00993 H281DRAFT_03016
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase H281DRAFT_01080 H281DRAFT_03954
rocA 1-pyrroline-5-carboxylate dehydrogenase H281DRAFT_02404 H281DRAFT_03016
rocD ornithine aminotransferase H281DRAFT_03179 H281DRAFT_06478

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.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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