GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Pseudarthrobacter sulfonivorans Ar51

Best path

rocE, arg-monooxygenase, gbamidase, kauB, gbuA, gabT, gabD

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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease AU252_RS04790 AU252_RS08100
arg-monooxygenase arginine 2-monooxygenase AU252_RS13885 AU252_RS04545
gbamidase guanidinobutyramidase AU252_RS04565 AU252_RS09230
kauB 4-guanidinobutyraldehyde dehydrogenase AU252_RS01555 AU252_RS22410
gbuA guanidinobutyrase AU252_RS05860
gabT gamma-aminobutyrate transaminase AU252_RS16125 AU252_RS02890
gabD succinate semialdehyde dehydrogenase AU252_RS01005 AU252_RS04095
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase AU252_RS06340 AU252_RS13115
aguB N-carbamoylputrescine hydrolase AU252_RS13110 AU252_RS06335
arcA arginine deiminase
arcB ornithine carbamoyltransferase AU252_RS02885 AU252_RS21000
arcC carbamate kinase
aroD L-arginine oxidase
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT AU252_RS05500
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) AU252_RS15205 AU252_RS09255
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA AU252_RS13385 AU252_RS13905
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) AU252_RS09255 AU252_RS13390
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase AU252_RS16745 AU252_RS19290
aruI 2-ketoarginine decarboxylase AU252_RS19110 AU252_RS01175
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase AU252_RS02890 AU252_RS16125
astD succinylglutamate semialdehyde dehydrogenase AU252_RS12795 AU252_RS07815
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase AU252_RS00950 AU252_RS16800
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AU252_RS04325
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AU252_RS04330
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) AU252_RS04335 AU252_RS00660
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) AU252_RS04340 AU252_RS01290
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 AU252_RS16215 AU252_RS04550
davD glutarate semialdehyde dehydrogenase AU252_RS01005 AU252_RS04095
davT 5-aminovalerate aminotransferase AU252_RS16125 AU252_RS02890
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AU252_RS07800 AU252_RS00745
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AU252_RS02130 AU252_RS07090
gcdG succinyl-CoA:glutarate CoA-transferase AU252_RS00300 AU252_RS01440
gcdH glutaryl-CoA dehydrogenase AU252_RS16430 AU252_RS00305
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) AU252_RS02890 AU252_RS16125
patD gamma-aminobutyraldehyde dehydrogenase AU252_RS16120 AU252_RS22315
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
PRO3 pyrroline-5-carboxylate reductase AU252_RS14565
puo putrescine oxidase AU252_RS10185
put1 proline dehydrogenase AU252_RS11615 AU252_RS09435
putA L-glutamate 5-semialdeyde dehydrogenase AU252_RS22410 AU252_RS01555
puuA glutamate-putrescine ligase AU252_RS13215 AU252_RS02415
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AU252_RS01555 AU252_RS22410
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase AU252_RS13210
rocA 1-pyrroline-5-carboxylate dehydrogenase AU252_RS22410 AU252_RS01555
rocD ornithine aminotransferase AU252_RS02890 AU252_RS16125
rocF arginase AU252_RS05860
speB agmatinase AU252_RS05860

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.

Links

Downloads

Related tools

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