GapMind for catabolism of small carbon sources


L-arginine catabolism in Marinomonas arctica 328

Best path

artJ, artM, artP, artQ, astA, astB, astC, astD, astE


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 (44 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 DK187_RS13620 DK187_RS16325
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) DK187_RS13630 DK187_RS16320
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA DK187_RS13615 DK187_RS16315
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) DK187_RS13625 DK187_RS13630
astA arginine N-succinyltransferase DK187_RS07635 DK187_RS07640
astB N-succinylarginine dihydrolase DK187_RS07625
astC succinylornithine transaminase DK187_RS13600 DK187_RS13845
astD succinylglutamate semialdehyde dehydrogenase DK187_RS07630 DK187_RS02405
astE succinylglutamate desuccinylase DK187_RS13660
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) DK187_RS07050
aguA agmatine deiminase DK187_RS08385
aguB N-carbamoylputrescine hydrolase DK187_RS07055
arcA arginine deiminase
arcB ornithine carbamoyltransferase DK187_RS00395 DK187_RS15935
arcC carbamate kinase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) DK187_RS07640 DK187_RS07635
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) DK187_RS07635 DK187_RS07640
aruH L-arginine:pyruvate transaminase DK187_RS08045 DK187_RS16805
aruI 2-ketoarginine decarboxylase
atoB acetyl-CoA C-acetyltransferase DK187_RS06190 DK187_RS08790
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 DK187_RS07505
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) DK187_RS07510
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) DK187_RS07515
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) DK187_RS07520 DK187_RS09960
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) DK187_RS07525 DK187_RS09965
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase DK187_RS02405 DK187_RS15780
davT 5-aminovalerate aminotransferase DK187_RS02410 DK187_RS13600
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase DK187_RS04965 DK187_RS08785
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase DK187_RS08785 DK187_RS04955
gabD succinate semialdehyde dehydrogenase DK187_RS02405 DK187_RS18540
gabT gamma-aminobutyrate transaminase DK187_RS02410 DK187_RS08575
gbamidase guanidinobutyramidase DK187_RS03955
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase DK187_RS07920
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase DK187_RS01055 DK187_RS00035
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) DK187_RS04730
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase DK187_RS12845
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) DK187_RS08575 DK187_RS13600
patD gamma-aminobutyraldehyde dehydrogenase DK187_RS01055 DK187_RS17920
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase DK187_RS02370
PRO3 pyrroline-5-carboxylate reductase DK187_RS15955
puo putrescine oxidase
put1 proline dehydrogenase DK187_RS02925
putA L-glutamate 5-semialdeyde dehydrogenase DK187_RS02925 DK187_RS15725
puuA glutamate-putrescine ligase DK187_RS01010 DK187_RS01045
puuB gamma-glutamylputrescine oxidase DK187_RS01050 DK187_RS01015
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase DK187_RS01055 DK187_RS00035
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase DK187_RS02925 DK187_RS15725
rocD ornithine aminotransferase DK187_RS02410 DK187_RS13985
rocE L-arginine permease
rocF arginase
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.



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