GapMind for catabolism of small carbon sources


L-arginine catabolism in Marinobacter adhaerens HP15

Best path

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

Also see fitness data for the top candidates


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 (47 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 HP15_3031 HP15_2918
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) HP15_3033 HP15_3032
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA HP15_3030 HP15_2920
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) HP15_3032 HP15_2919
astA arginine N-succinyltransferase HP15_3040 HP15_3041
astB N-succinylarginine dihydrolase HP15_3038
astC succinylornithine transaminase HP15_3042 HP15_3708
astD succinylglutamate semialdehyde dehydrogenase HP15_3039 HP15_3945
astE succinylglutamate desuccinylase HP15_3034
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) HP15_272
aguA agmatine deiminase HP15_2073
aguB N-carbamoylputrescine hydrolase HP15_2074
arcA arginine deiminase HP15_3986
arcB ornithine carbamoyltransferase HP15_3987 HP15_750
arcC carbamate kinase HP15_3988
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) HP15_3041 HP15_3040
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) HP15_3040 HP15_3041
aruH L-arginine:pyruvate transaminase HP15_1371 HP15_814
aruI 2-ketoarginine decarboxylase HP15_1017
atoB acetyl-CoA C-acetyltransferase HP15_2996 HP15_5
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 HP15_3055
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) HP15_3056 HP15_2706
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) HP15_3057 HP15_4097
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) HP15_3058 HP15_4095
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) HP15_3059 HP15_2703
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase HP15_2020 HP15_3404
davT 5-aminovalerate aminotransferase HP15_3708 HP15_3042
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HP15_908 HP15_12
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HP15_1512 HP15_3941
gabD succinate semialdehyde dehydrogenase HP15_3404 HP15_2020
gabT gamma-aminobutyrate transaminase HP15_3708 HP15_2925
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase HP15_1416 HP15_2609
gcdH glutaryl-CoA dehydrogenase HP15_3936 HP15_2
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase HP15_943 HP15_3144
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) HP15_2488
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase HP15_3785
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) HP15_2925 HP15_3042
patD gamma-aminobutyraldehyde dehydrogenase HP15_943 HP15_3626
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 HP15_287
puo putrescine oxidase
put1 proline dehydrogenase HP15_2688
putA L-glutamate 5-semialdeyde dehydrogenase HP15_2688 HP15_3626
puuA glutamate-putrescine ligase HP15_942 HP15_428
puuB gamma-glutamylputrescine oxidase HP15_944
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase HP15_943 HP15_3144
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase HP15_2338
rocA 1-pyrroline-5-carboxylate dehydrogenase HP15_2688 HP15_3626
rocD ornithine aminotransferase HP15_3708 HP15_3855
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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