GapMind for catabolism of small carbon sources


L-citrulline catabolism in Dinoroseobacter shibae DFL-12

Best path

PS417_17590, PS417_17595, PS417_17600, PS417_17605, 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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1 Dshi_2223 Dshi_2224
PS417_17600 ABC transporter for L-Citrulline, permease component 2 Dshi_2224
PS417_17605 ABC transporter for L-Citrulline, ATPase component Dshi_2221 Dshi_0321
arcB ornithine carbamoyltransferase Dshi_0433 Dshi_0796
arcC carbamate kinase Dshi_0434
ocd ornithine cyclodeaminase Dshi_2310 Dshi_0890
put1 proline dehydrogenase Dshi_2311
putA L-glutamate 5-semialdeyde dehydrogenase Dshi_2311 Dshi_0577
Alternative steps:
AO353_03040 ABC transporter for L-Citrulline, ATPase component Dshi_2221 Dshi_0321
AO353_03045 ABC transporter for L-Citrulline, permease component 2 Dshi_2224
AO353_03050 ABC transporter for L-Citrulline, permease component 1 Dshi_2223 Dshi_2224
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component Dshi_2222
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase Dshi_0798 Dshi_1446
astD succinylglutamate semialdehyde dehydrogenase Dshi_1425 Dshi_0577
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Dshi_3066 Dshi_3331
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase Dshi_2887 Dshi_0577
davT 5-aminovalerate aminotransferase Dshi_1446 Dshi_0798
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Dshi_3370 Dshi_0835
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Dshi_3826 Dshi_0835
gabD succinate semialdehyde dehydrogenase Dshi_2887 Dshi_1430
gabT gamma-aminobutyrate transaminase Dshi_1366 Dshi_2042
gcdG succinyl-CoA:glutarate CoA-transferase Dshi_3269 Dshi_1057
gcdH glutaryl-CoA dehydrogenase Dshi_2357 Dshi_1297
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
odc L-ornithine decarboxylase Dshi_1375
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 Dshi_2298
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) Dshi_1366 Dshi_2042
patD gamma-aminobutyraldehyde dehydrogenase Dshi_1095 Dshi_3017
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 Dshi_2645
puo putrescine oxidase
puuA glutamate-putrescine ligase Dshi_2226 Dshi_1839
puuB gamma-glutamylputrescine oxidase Dshi_2227
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Dshi_1430 Dshi_3017
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Dshi_1229 Dshi_3925
rocA 1-pyrroline-5-carboxylate dehydrogenase Dshi_2311 Dshi_0577
rocD ornithine aminotransferase Dshi_2042 Dshi_1366

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