GapMind for catabolism of small carbon sources


L-arginine catabolism in Azospirillum brasilense Sp245

Best path

braC, braD, braE, braF, braG, arcA, arcB, arcC, rocD, PRO3, 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 (48 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 AZOBR_RS08260
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AZOBR_RS08235 AZOBR_RS03565
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AZOBR_RS08240 AZOBR_RS32410
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) AZOBR_RS08245 AZOBR_RS32405
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) AZOBR_RS08250 AZOBR_RS19790
arcA arginine deiminase AZOBR_RS13255
arcB ornithine carbamoyltransferase AZOBR_RS13250 AZOBR_RS19030
arcC carbamate kinase AZOBR_RS13245
rocD ornithine aminotransferase AZOBR_RS19590 AZOBR_RS19630
PRO3 pyrroline-5-carboxylate reductase AZOBR_RS06245
put1 proline dehydrogenase AZOBR_RS23695
putA L-glutamate 5-semialdeyde dehydrogenase AZOBR_RS23695 AZOBR_RS29185
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) AZOBR_RS27535 AZOBR_RS00105
aguA agmatine deiminase AZOBR_RS08825
aguB N-carbamoylputrescine hydrolase AZOBR_RS08170 AZOBR_RS30770
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT AZOBR_RS27130 AZOBR_RS00685
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) AZOBR_RS00675 AZOBR_RS23520
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA AZOBR_RS00690 AZOBR_RS29615
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) AZOBR_RS00680 AZOBR_RS23520
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase AZOBR_RS24065 AZOBR_RS12970
aruI 2-ketoarginine decarboxylase AZOBR_RS04230
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase AZOBR_RS19025 AZOBR_RS19590
astD succinylglutamate semialdehyde dehydrogenase AZOBR_RS09720 AZOBR_RS19635
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase AZOBR_RS30610 AZOBR_RS28180
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 AZOBR_RS09720 AZOBR_RS19635
davT 5-aminovalerate aminotransferase AZOBR_RS19630 AZOBR_RS19025
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AZOBR_RS01260 AZOBR_RS26485
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AZOBR_RS20225 AZOBR_RS29225
gabD succinate semialdehyde dehydrogenase AZOBR_RS09720 AZOBR_RS19635
gabT gamma-aminobutyrate transaminase AZOBR_RS19630 AZOBR_RS03635
gbamidase guanidinobutyramidase AZOBR_RS30770
gbuA guanidinobutyrase AZOBR_RS30775 AZOBR_RS30430
gcdG succinyl-CoA:glutarate CoA-transferase AZOBR_RS19675 AZOBR_RS29180
gcdH glutaryl-CoA dehydrogenase AZOBR_RS19670 AZOBR_RS22310
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase AZOBR_RS09720 AZOBR_RS19635
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) AZOBR_RS33525
ocd ornithine cyclodeaminase AZOBR_RS03120
odc L-ornithine decarboxylase AZOBR_RS27535 AZOBR_RS00105
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) AZOBR_RS03635 AZOBR_RS22505
patD gamma-aminobutyraldehyde dehydrogenase AZOBR_RS22315 AZOBR_RS19635
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase AZOBR_RS27830
puo putrescine oxidase
puuA glutamate-putrescine ligase AZOBR_RS08850
puuB gamma-glutamylputrescine oxidase AZOBR_RS08855 AZOBR_RS25655
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AZOBR_RS09720 AZOBR_RS19635
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase AZOBR_RS02010 AZOBR_RS00395
rocA 1-pyrroline-5-carboxylate dehydrogenase AZOBR_RS23695 AZOBR_RS29185
rocE L-arginine permease
rocF arginase AZOBR_RS19585 AZOBR_RS30775
speB agmatinase AZOBR_RS30775 AZOBR_RS30430

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