GapMind for catabolism of small carbon sources


L-arginine catabolism in Herbaspirillum seropedicae SmR1

Best path

braC, braD, braE, braF, braG, rocF, ocd, put1, putA

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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC HSERO_RS08270 HSERO_RS17350
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) HSERO_RS08275 HSERO_RS05960
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) HSERO_RS08280 HSERO_RS05965
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) HSERO_RS08285 HSERO_RS20055
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) HSERO_RS08290 HSERO_RS05975
rocF arginase HSERO_RS00305 HSERO_RS08555
ocd ornithine cyclodeaminase HSERO_RS00300 HSERO_RS22840
put1 proline dehydrogenase HSERO_RS00905 HSERO_RS05695
putA L-glutamate 5-semialdeyde dehydrogenase HSERO_RS00905 HSERO_RS11260
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) HSERO_RS17280
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase HSERO_RS07185 HSERO_RS02330
arcC carbamate kinase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT HSERO_RS10775 HSERO_RS21615
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) HSERO_RS11445 HSERO_RS23035
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA HSERO_RS00320 HSERO_RS05835
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) HSERO_RS10770 HSERO_RS05830
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase HSERO_RS15115 HSERO_RS10805
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase HSERO_RS16670 HSERO_RS17580
astD succinylglutamate semialdehyde dehydrogenase HSERO_RS05395 HSERO_RS11260
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase HSERO_RS01180 HSERO_RS04635
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase HSERO_RS05395 HSERO_RS05645
davT 5-aminovalerate aminotransferase HSERO_RS05420 HSERO_RS19685
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HSERO_RS19405 HSERO_RS20665
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HSERO_RS01260 HSERO_RS04630
gabD succinate semialdehyde dehydrogenase HSERO_RS07235 HSERO_RS05645
gabT gamma-aminobutyrate transaminase HSERO_RS05420 HSERO_RS05635
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase HSERO_RS08555
gcdG succinyl-CoA:glutarate CoA-transferase HSERO_RS18350 HSERO_RS14050
gcdH glutaryl-CoA dehydrogenase HSERO_RS23440 HSERO_RS04640
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase HSERO_RS09465 HSERO_RS19755
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) HSERO_RS21645
odc L-ornithine decarboxylase HSERO_RS17280
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) HSERO_RS05635 HSERO_RS23240
patD gamma-aminobutyraldehyde dehydrogenase HSERO_RS19755 HSERO_RS09465
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase HSERO_RS00875
PRO3 pyrroline-5-carboxylate reductase HSERO_RS18990
puo putrescine oxidase HSERO_RS17625
puuA glutamate-putrescine ligase HSERO_RS15690
puuB gamma-glutamylputrescine oxidase HSERO_RS01275 HSERO_RS05840
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase HSERO_RS09465 HSERO_RS19755
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase HSERO_RS21960
rocA 1-pyrroline-5-carboxylate dehydrogenase HSERO_RS00905 HSERO_RS11260
rocD ornithine aminotransferase HSERO_RS19685 HSERO_RS05420
rocE L-arginine permease
speB agmatinase HSERO_RS08555

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:

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