GapMind for catabolism of small carbon sources


L-citrulline catabolism in Escherichia coli BW25113

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component b2310 b2309
AO353_03050 ABC transporter for L-Citrulline, permease component 1 b2308 b0862
AO353_03045 ABC transporter for L-Citrulline, permease component 2 b2307 b0861
AO353_03040 ABC transporter for L-Citrulline, ATPase component b2306 b0809
arcB ornithine carbamoyltransferase b0273 b4254
arcC carbamate kinase b0521 b2874
odc L-ornithine decarboxylase b0693 b2965
puuA glutamate-putrescine ligase b1297 b3870
puuB gamma-glutamylputrescine oxidase b1301
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase b1300 b3588
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase b1298
gabT gamma-aminobutyrate transaminase b2662 b1302
gabD succinate semialdehyde dehydrogenase b1300 b2661
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) b1747
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) b1747
astC succinylornithine transaminase b1748 b3359
astD succinylglutamate semialdehyde dehydrogenase b1746 b2661
astE succinylglutamate desuccinylase b1744
atoB acetyl-CoA C-acetyltransferase b2224 b2844
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase b2661 b1415
davT 5-aminovalerate aminotransferase b2662 b1302
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase b1393 b3846
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase b3846 b2341
gcdG succinyl-CoA:glutarate CoA-transferase b2371 b2374
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) b2659
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) b2660
ocd ornithine cyclodeaminase
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) b3073 b1302
patD gamma-aminobutyraldehyde dehydrogenase b1444 b1300
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
PRO3 pyrroline-5-carboxylate reductase b0386
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component b2309 b2310
PS417_17595 ABC transporter for L-Citrulline, permease component 1 b2308 b0862
PS417_17600 ABC transporter for L-Citrulline, permease component 2 b2307 b0861
PS417_17605 ABC transporter for L-Citrulline, ATPase component b2306 b0809
puo putrescine oxidase b1386
put1 proline dehydrogenase b1014
putA L-glutamate 5-semialdeyde dehydrogenase b1014 b1415
rocA 1-pyrroline-5-carboxylate dehydrogenase b1014 b1415
rocD ornithine aminotransferase b1302 b2662

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