GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Sphingomonas indica Dd16

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component
AO353_03050 ABC transporter for L-Citrulline, permease component 1
AO353_03045 ABC transporter for L-Citrulline, permease component 2
AO353_03040 ABC transporter for L-Citrulline, ATPase component B9N75_RS12690 B9N75_RS06700
citrullinase putative citrullinase B9N75_RS01320
rocD ornithine aminotransferase B9N75_RS01575
PRO3 pyrroline-5-carboxylate reductase B9N75_RS07535
put1 proline dehydrogenase B9N75_RS04120
putA L-glutamate 5-semialdeyde dehydrogenase B9N75_RS04120 B9N75_RS04360
Alternative steps:
arcB ornithine carbamoyltransferase B9N75_RS11350 B9N75_RS13240
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) B9N75_RS09775
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) B9N75_RS09775
astC succinylornithine transaminase B9N75_RS01575
astD succinylglutamate semialdehyde dehydrogenase B9N75_RS13395 B9N75_RS04120
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase B9N75_RS12685 B9N75_RS02915
davD glutarate semialdehyde dehydrogenase B9N75_RS04360 B9N75_RS09590
davT 5-aminovalerate aminotransferase B9N75_RS01575
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase B9N75_RS13460 B9N75_RS11255
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase B9N75_RS08655 B9N75_RS11255
gabD succinate semialdehyde dehydrogenase B9N75_RS04360 B9N75_RS09590
gabT gamma-aminobutyrate transaminase B9N75_RS01575
gcdG succinyl-CoA:glutarate CoA-transferase B9N75_RS12190
gcdH glutaryl-CoA dehydrogenase B9N75_RS12195 B9N75_RS13160
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase B9N75_RS13195
odc L-ornithine decarboxylase B9N75_RS00125
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) B9N75_RS01575
patD gamma-aminobutyraldehyde dehydrogenase B9N75_RS04360 B9N75_RS00315
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase B9N75_RS00310
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595 ABC transporter for L-Citrulline, permease component 1
PS417_17600 ABC transporter for L-Citrulline, permease component 2
PS417_17605 ABC transporter for L-Citrulline, ATPase component B9N75_RS12690 B9N75_RS12890
puo putrescine oxidase
puuA glutamate-putrescine ligase B9N75_RS03460
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase B9N75_RS04360 B9N75_RS00315
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase B9N75_RS04120 B9N75_RS04360

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 24 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