GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Flavobacterium glycines Gm-149

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 (20 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 BLR17_RS12145 BLR17_RS06945
citrullinase putative citrullinase BLR17_RS11365 BLR17_RS10025
rocD ornithine aminotransferase BLR17_RS15165 BLR17_RS09610
PRO3 pyrroline-5-carboxylate reductase BLR17_RS01955
put1 proline dehydrogenase BLR17_RS14180
putA L-glutamate 5-semialdeyde dehydrogenase BLR17_RS05765
Alternative steps:
arcB ornithine carbamoyltransferase BLR17_RS14815 BLR17_RS14895
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC succinylornithine transaminase BLR17_RS15165 BLR17_RS14830
astD succinylglutamate semialdehyde dehydrogenase
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase BLR17_RS08645 BLR17_RS15680
davD glutarate semialdehyde dehydrogenase
davT 5-aminovalerate aminotransferase BLR17_RS15165 BLR17_RS09610
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLR17_RS02485 BLR17_RS04170
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLR17_RS15685 BLR17_RS09950
gabD succinate semialdehyde dehydrogenase BLR17_RS03500
gabT gamma-aminobutyrate transaminase BLR17_RS15165 BLR17_RS09610
gcdG succinyl-CoA:glutarate CoA-transferase BLR17_RS03135
gcdH glutaryl-CoA dehydrogenase BLR17_RS01000 BLR17_RS11710
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase
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) BLR17_RS15165 BLR17_RS09610
patD gamma-aminobutyraldehyde dehydrogenase
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase BLR17_RS04950
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 BLR17_RS06945 BLR17_RS13460
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase BLR17_RS05765

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