GapMind for catabolism of small carbon sources


L-arginine catabolism in Sinorhizobium meliloti 1021

Best path

braC, braD, braE, braF, braG, arcA, arcB, arcC, 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 (47 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 SMc01946 SMc00078
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) SMc01951 SMc02359
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) SMc01950
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) SMc01949 SMc02357
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) SMc01948 SMc02358
arcA arginine deiminase SMa1670 SMa0693
arcB ornithine carbamoyltransferase SMa0695 SMc02137
arcC carbamate kinase SMa0697
ocd ornithine cyclodeaminase SM_b21494 SMa1871
put1 proline dehydrogenase SMc02181
putA L-glutamate 5-semialdeyde dehydrogenase SMc02181 SM_b20891
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) SMa0682 SMa0680
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase SMc01962
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT SM_b20706 SMc00140
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) SMa0492 SMc00138
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA SMc02260 SM_b21138
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) SMc02258 SMc00139
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase SMc02262 SMc01578
aruI 2-ketoarginine decarboxylase SMc02263 SM_b20681
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase SMc02138 SM_b21186
astD succinylglutamate semialdehyde dehydrogenase SMc02780 SM_b20891
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase SMc03879 SMa1450
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 SMc02780 SMa0805
davT 5-aminovalerate aminotransferase SM_b21186 SMc02413
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SMc01153 SMc01669
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SMc02227 SMc00727
gabD succinate semialdehyde dehydrogenase SMc02780 SMa0805
gabT gamma-aminobutyrate transaminase SM_b21186 SM_b20379
gbamidase guanidinobutyramidase SMc01962 SMc02442
gbuA guanidinobutyrase SMc01967 SMc01802
gcdG succinyl-CoA:glutarate CoA-transferase SM_b21182 SM_b21089
gcdH glutaryl-CoA dehydrogenase SM_b21181 SM_b21121
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase SMa1415 SMc02689
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) SM_b20101
odc L-ornithine decarboxylase SMa0680 SMc02983
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) SMa1855 SM_b20379
patD gamma-aminobutyraldehyde dehydrogenase SMc01656 SMc00094
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase SM_b20268 SM_b20270
PRO3 pyrroline-5-carboxylate reductase SMc02677
puo putrescine oxidase
puuA glutamate-putrescine ligase SMc00762 SMc01973
puuB gamma-glutamylputrescine oxidase SMc01972 SMc03132
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase SMa1415 SMc02689
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase SMc03943
rocA 1-pyrroline-5-carboxylate dehydrogenase SMc02181 SM_b20891
rocD ornithine aminotransferase SM_b21186 SMc02138
rocE L-arginine permease
rocF arginase SMc03091 SMc01967
speB agmatinase SMc01802 SMc01967

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