GapMind for catabolism of small carbon sources


L-citrulline catabolism in Sinorhizobium meliloti 1021

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component SMc02259 SMc00140
AO353_03050 ABC transporter for L-Citrulline, permease component 1 SMc02258 SMc00139
AO353_03045 ABC transporter for L-Citrulline, permease component 2 SMa0492 SMc02257
AO353_03040 ABC transporter for L-Citrulline, ATPase component SMc02260 SM_b21138
arcB ornithine carbamoyltransferase SMa0695 SMc02137
arcC carbamate kinase SMa0697
ocd ornithine cyclodeaminase SM_b21494 SMa1871
put1 proline dehydrogenase SMc02181
putA L-glutamate 5-semialdeyde dehydrogenase SMc02181 SM_b20891
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase SMc02138 SM_b21186
astD succinylglutamate semialdehyde dehydrogenase SMc02780 SM_b20891
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase SMc03879 SMa1450
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase SMc02780 SMa0805
davT 5-aminovalerate aminotransferase SM_b21186 SMc02413
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SMc01153 SMc01669
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SMc02227 SMc00727
gabD succinate semialdehyde dehydrogenase SMc02780 SMa0805
gabT gamma-aminobutyrate transaminase SM_b21186 SM_b20379
gcdG succinyl-CoA:glutarate CoA-transferase SM_b21182 SM_b21089
gcdH glutaryl-CoA dehydrogenase SM_b21181 SM_b21121
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) SM_b20101
odc L-ornithine decarboxylase SMa0680 SMc02983
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) SMa1855 SM_b20379
patD gamma-aminobutyraldehyde dehydrogenase SMc01656 SMc00094
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase SM_b20268 SM_b20270
PRO3 pyrroline-5-carboxylate reductase SMc02677
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component SMc02259 SMc00140
PS417_17595 ABC transporter for L-Citrulline, permease component 1 SMc00139 SMc02258
PS417_17600 ABC transporter for L-Citrulline, permease component 2 SMa0492 SMc00138
PS417_17605 ABC transporter for L-Citrulline, ATPase component SMc02260 SM_b21138
puo putrescine oxidase
puuA glutamate-putrescine ligase SMc00762 SMc01973
puuB gamma-glutamylputrescine oxidase SMc01972 SMc03132
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase SMa1415 SMc02689
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase SMc03943
rocA 1-pyrroline-5-carboxylate dehydrogenase SMc02181 SM_b20891
rocD ornithine aminotransferase SM_b21186 SMc02138

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