GapMind for catabolism of small carbon sources


L-citrulline catabolism in Phaeobacter inhibens BS107

Best path

PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, 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
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component PGA1_262p02360
PS417_17595 ABC transporter for L-Citrulline, permease component 1 PGA1_262p02370 PGA1_c26600
PS417_17600 ABC transporter for L-Citrulline, permease component 2 PGA1_c11550 PGA1_262p02380
PS417_17605 ABC transporter for L-Citrulline, ATPase component PGA1_262p02350 PGA1_c11580
citrullinase putative citrullinase PGA1_c16380
ocd ornithine cyclodeaminase PGA1_c16390
put1 proline dehydrogenase PGA1_c11750 PGA1_c23300
putA L-glutamate 5-semialdeyde dehydrogenase PGA1_c11750 PGA1_c05130
Alternative steps:
AO353_03040 ABC transporter for L-Citrulline, ATPase component PGA1_262p02350 PGA1_c11580
AO353_03045 ABC transporter for L-Citrulline, permease component 2 PGA1_262p02380 PGA1_65p00120
AO353_03050 ABC transporter for L-Citrulline, permease component 1 PGA1_262p02370 PGA1_c11560
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component PGA1_262p02360 PGA1_65p00110
arcB ornithine carbamoyltransferase PGA1_c24220 PGA1_c03060
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase PGA1_c24230 PGA1_c28750
astD succinylglutamate semialdehyde dehydrogenase PGA1_c32120 PGA1_262p01460
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase PGA1_c03400 PGA1_c33180
davD glutarate semialdehyde dehydrogenase PGA1_c29650 PGA1_c23170
davT 5-aminovalerate aminotransferase PGA1_c24230 PGA1_c28750
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PGA1_c36500 PGA1_262p01980
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PGA1_c04110 PGA1_c11320
gabD succinate semialdehyde dehydrogenase PGA1_c29650 PGA1_c23170
gabT gamma-aminobutyrate transaminase PGA1_c34400 PGA1_c09350
gcdG succinyl-CoA:glutarate CoA-transferase PGA1_c27870 PGA1_c12340
gcdH glutaryl-CoA dehydrogenase PGA1_c15710 PGA1_c10280
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
odc L-ornithine decarboxylase PGA1_c11650 PGA1_c03800
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 PGA1_c17610
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) PGA1_c34400 PGA1_c09350
patD gamma-aminobutyraldehyde dehydrogenase PGA1_c21670 PGA1_c32250
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase PGA1_262p00280 PGA1_c05120
PRO3 pyrroline-5-carboxylate reductase PGA1_c24700
puo putrescine oxidase
puuA glutamate-putrescine ligase PGA1_c11520 PGA1_c11540
puuB gamma-glutamylputrescine oxidase PGA1_c11510 PGA1_78p00350
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PGA1_c32250 PGA1_c21670
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase PGA1_c09920 PGA1_c28350
rocA 1-pyrroline-5-carboxylate dehydrogenase PGA1_c11750 PGA1_c05130
rocD ornithine aminotransferase PGA1_c28770 PGA1_c09350

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