GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Paucidesulfovibrio gracilis DSM 16080

Best path

braC, braD, braE, braF, braG, rocF, rocD, rocA

Rules

Overview: Arginine utilization in GapMind is based on MetaCyc pathways L-arginine degradation I via arginase (link); II via arginine succinyltransferase (link), III via arginine decarboxylase and agmatinase (link), IV via arginine decarboxylase and agmatine deiminase (link), V via arginine deiminase (link), VI (arginase 2, link), VII (arginase 3, link), VIII via arginase oxidase (link), IX via arginine:pyruvate transaminase (link), X via arginine monooxygenase (link), XIII via proline (link), and XIV via D-ornithine (link). Common intermediates are L-ornithine or L-proline. GapMind does not include pathways XI (link), which is poorly understood, or XII (link), which is not reported in prokaryotes.

71 steps (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC B5D49_RS04220 B5D49_RS00095
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) B5D49_RS00090 B5D49_RS04225
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) B5D49_RS00085 B5D49_RS04230
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) B5D49_RS04215 B5D49_RS00080
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) B5D49_RS00075 B5D49_RS04235
rocF arginase
rocD ornithine aminotransferase B5D49_RS12615 B5D49_RS03155
rocA 1-pyrroline-5-carboxylate dehydrogenase B5D49_RS04205 B5D49_RS13965
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase B5D49_RS05365 B5D49_RS12320
arcC carbamate kinase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT B5D49_RS01065 B5D49_RS02705
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) B5D49_RS01060 B5D49_RS12105
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA B5D49_RS02695 B5D49_RS05290
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) B5D49_RS10255 B5D49_RS01060
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase B5D49_RS13990 B5D49_RS10555
aruI 2-ketoarginine decarboxylase B5D49_RS07175
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase B5D49_RS05850 B5D49_RS12615
astD succinylglutamate semialdehyde dehydrogenase B5D49_RS13965 B5D49_RS04205
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase B5D49_RS03160
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase B5D49_RS13965 B5D49_RS04205
davT 5-aminovalerate aminotransferase B5D49_RS03155 B5D49_RS12615
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase B5D49_RS01965
gabD succinate semialdehyde dehydrogenase B5D49_RS13965 B5D49_RS04205
gabT gamma-aminobutyrate transaminase B5D49_RS03155 B5D49_RS14700
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase B5D49_RS13965 B5D49_RS04205
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) B5D49_RS12670
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) B5D49_RS14700 B5D49_RS12615
patD gamma-aminobutyraldehyde dehydrogenase B5D49_RS13965 B5D49_RS04205
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase B5D49_RS03205
PRO3 pyrroline-5-carboxylate reductase B5D49_RS05795 B5D49_RS00655
puo putrescine oxidase
put1 proline dehydrogenase B5D49_RS04205
putA L-glutamate 5-semialdeyde dehydrogenase B5D49_RS04205 B5D49_RS13965
puuA glutamate-putrescine ligase B5D49_RS13465
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase B5D49_RS13965 B5D49_RS04205
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase B5D49_RS13775
rocE L-arginine permease
speB agmatinase

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 Apr 09 2024. 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