GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Marivita geojedonensis DPG-138

Best path

artJ, artM, artP, artQ, aruH, aruI, 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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT MGEO_RS13230 MGEO_RS07805
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) MGEO_RS13240 MGEO_RS07795
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA MGEO_RS13225 MGEO_RS08670
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) MGEO_RS13235 MGEO_RS07800
aruH L-arginine:pyruvate transaminase MGEO_RS06340 MGEO_RS15180
aruI 2-ketoarginine decarboxylase MGEO_RS19930
kauB 4-guanidinobutyraldehyde dehydrogenase MGEO_RS07470 MGEO_RS12055
gbuA guanidinobutyrase MGEO_RS14950 MGEO_RS18820
gabT gamma-aminobutyrate transaminase MGEO_RS06140 MGEO_RS01105
gabD succinate semialdehyde dehydrogenase MGEO_RS15320 MGEO_RS02345
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 MGEO_RS04590 MGEO_RS01990
arcC carbamate kinase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase MGEO_RS04585 MGEO_RS10805
astD succinylglutamate semialdehyde dehydrogenase MGEO_RS04980 MGEO_RS00465
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase MGEO_RS09905 MGEO_RS17560
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) MGEO_RS18500
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) MGEO_RS04005 MGEO_RS05255
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) MGEO_RS05250 MGEO_RS04030
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase MGEO_RS15320 MGEO_RS02345
davT 5-aminovalerate aminotransferase MGEO_RS15340 MGEO_RS10195
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase MGEO_RS17480 MGEO_RS15835
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase MGEO_RS15835 MGEO_RS14675
gbamidase guanidinobutyramidase MGEO_RS06590
gcdG succinyl-CoA:glutarate CoA-transferase MGEO_RS11950 MGEO_RS18005
gcdH glutaryl-CoA dehydrogenase MGEO_RS11945 MGEO_RS05735
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase MGEO_RS13255 MGEO_RS07770
odc L-ornithine decarboxylase MGEO_RS00185
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 MGEO_RS07780
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) MGEO_RS01105 MGEO_RS06140
patD gamma-aminobutyraldehyde dehydrogenase MGEO_RS17260 MGEO_RS07470
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase MGEO_RS01160
PRO3 pyrroline-5-carboxylate reductase MGEO_RS00580
puo putrescine oxidase
put1 proline dehydrogenase MGEO_RS16525
putA L-glutamate 5-semialdeyde dehydrogenase MGEO_RS16525 MGEO_RS17260
puuA glutamate-putrescine ligase MGEO_RS08640 MGEO_RS08650
puuB gamma-glutamylputrescine oxidase MGEO_RS08635
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase MGEO_RS07470 MGEO_RS12055
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase MGEO_RS16415 MGEO_RS19085
rocA 1-pyrroline-5-carboxylate dehydrogenase MGEO_RS16525 MGEO_RS17260
rocD ornithine aminotransferase MGEO_RS15340 MGEO_RS10195
rocE L-arginine permease
rocF arginase MGEO_RS16110 MGEO_RS14950
speB agmatinase MGEO_RS07790 MGEO_RS18820

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.

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