GapMind for catabolism of small carbon sources


L-arginine catabolism in Oceanisphaera arctica V1-41

Best path

artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD


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 (51 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 UN63_RS13380 UN63_RS02420
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) UN63_RS03175 UN63_RS13370
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA UN63_RS03190 UN63_RS13385
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) UN63_RS13375 UN63_RS03180
adiA arginine decarboxylase (AdiA/SpeA) UN63_RS01430 UN63_RS14765
aguA agmatine deiminase UN63_RS03760
aguB N-carbamoylputrescine hydrolase UN63_RS03755
puuA glutamate-putrescine ligase UN63_RS03990 UN63_RS03995
puuB gamma-glutamylputrescine oxidase UN63_RS14970 UN63_RS04000
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase UN63_RS09060 UN63_RS14965
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase UN63_RS09905 UN63_RS07980
gabT gamma-aminobutyrate transaminase UN63_RS03985 UN63_RS03445
gabD succinate semialdehyde dehydrogenase UN63_RS08090 UN63_RS03450
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase UN63_RS14305
arcB ornithine carbamoyltransferase UN63_RS13060 UN63_RS14300
arcC carbamate kinase UN63_RS14295
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) UN63_RS03530
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) UN63_RS03530
aruH L-arginine:pyruvate transaminase
aruI 2-ketoarginine decarboxylase UN63_RS06885
astA arginine N-succinyltransferase UN63_RS03530
astB N-succinylarginine dihydrolase UN63_RS04100
astC succinylornithine transaminase UN63_RS03535 UN63_RS03445
astD succinylglutamate semialdehyde dehydrogenase UN63_RS03525 UN63_RS09060
astE succinylglutamate desuccinylase UN63_RS04150
atoB acetyl-CoA C-acetyltransferase UN63_RS04220 UN63_RS09000
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 UN63_RS11720
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) UN63_RS11725
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) UN63_RS11730
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) UN63_RS11735 UN63_RS11740
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) UN63_RS11740 UN63_RS06410
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase UN63_RS08090 UN63_RS03450
davT 5-aminovalerate aminotransferase UN63_RS03445 UN63_RS03535
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase UN63_RS10750 UN63_RS14495
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase UN63_RS14495 UN63_RS01710
gbamidase guanidinobutyramidase UN63_RS03755
gbuA guanidinobutyrase UN63_RS16495
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase UN63_RS13340 UN63_RS08990
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) UN63_RS15945
kauB 4-guanidinobutyraldehyde dehydrogenase UN63_RS09060 UN63_RS14965
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) UN63_RS15950
ocd ornithine cyclodeaminase UN63_RS12655
odc L-ornithine decarboxylase UN63_RS14765
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) UN63_RS03985 UN63_RS05125
patD gamma-aminobutyraldehyde dehydrogenase UN63_RS14965 UN63_RS09060
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase UN63_RS09040
PRO3 pyrroline-5-carboxylate reductase UN63_RS05200
puo putrescine oxidase
put1 proline dehydrogenase UN63_RS01445 UN63_RS05380 with UN63_RS06480
putA L-glutamate 5-semialdeyde dehydrogenase UN63_RS01445 UN63_RS05380 with UN63_RS06480
rocA 1-pyrroline-5-carboxylate dehydrogenase UN63_RS01445 UN63_RS05380 with UN63_RS06480
rocD ornithine aminotransferase UN63_RS03445 UN63_RS03985
rocE L-arginine permease
rocF arginase
speB agmatinase UN63_RS16495

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.



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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