GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Cupriavidus basilensis 4G11

Best path

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

Also see fitness data for the top candidates

Rules

Overview: Citrulline can be catabolized via ornithine carbamoyltransferase in reverse (PMID:3129535). Genetic evidence suggests that some bacteria use a putative citrullinase (EC 3.5.1.20) to consume citrulline.

51 steps (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component RR42_RS29645 RR42_RS31745
AO353_03050 ABC transporter for L-Citrulline, permease component 1 RR42_RS29650 RR42_RS04400
AO353_03045 ABC transporter for L-Citrulline, permease component 2 RR42_RS29655 RR42_RS04400
AO353_03040 ABC transporter for L-Citrulline, ATPase component RR42_RS29660 RR42_RS34305
arcB ornithine carbamoyltransferase RR42_RS17175 RR42_RS15860
arcC carbamate kinase
ocd ornithine cyclodeaminase RR42_RS03960 RR42_RS29670
put1 proline dehydrogenase RR42_RS20125
putA L-glutamate 5-semialdeyde dehydrogenase RR42_RS20125 RR42_RS27350
Alternative steps:
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase RR42_RS16955 RR42_RS26240
astD succinylglutamate semialdehyde dehydrogenase RR42_RS26255 RR42_RS21375
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase RR42_RS07610 RR42_RS25455
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase RR42_RS21760 RR42_RS24555
davT 5-aminovalerate aminotransferase RR42_RS26160 RR42_RS26240
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RR42_RS18250 RR42_RS23710
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RR42_RS02510 RR42_RS36415
gabD succinate semialdehyde dehydrogenase RR42_RS26155 RR42_RS21760
gabT gamma-aminobutyrate transaminase RR42_RS26160 RR42_RS26240
gcdG succinyl-CoA:glutarate CoA-transferase RR42_RS15155 RR42_RS36540
gcdH glutaryl-CoA dehydrogenase RR42_RS15400 RR42_RS28565
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) RR42_RS06495
odc L-ornithine decarboxylase RR42_RS15940
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) RR42_RS27405 RR42_RS01575
patD gamma-aminobutyraldehyde dehydrogenase RR42_RS26255 RR42_RS21485
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase RR42_RS36345
PRO3 pyrroline-5-carboxylate reductase RR42_RS17360
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component RR42_RS29645
PS417_17595 ABC transporter for L-Citrulline, permease component 1 RR42_RS29650 RR42_RS04400
PS417_17600 ABC transporter for L-Citrulline, permease component 2 RR42_RS29655 RR42_RS00255
PS417_17605 ABC transporter for L-Citrulline, ATPase component RR42_RS29660 RR42_RS07815
puo putrescine oxidase RR42_RS24640 RR42_RS24620
puuA glutamate-putrescine ligase RR42_RS12995
puuB gamma-glutamylputrescine oxidase RR42_RS34300 RR42_RS07820
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase RR42_RS21485 RR42_RS26255
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase RR42_RS20125 RR42_RS27350
rocD ornithine aminotransferase RR42_RS26240 RR42_RS21370

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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