GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Sinorhizobium fredii NGR234

Best path

braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA

Rules

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 (46 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 NGR_RS23720 NGR_RS14075
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) NGR_RS23745 NGR_RS10925
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) NGR_RS23740 NGR_RS28285
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) NGR_RS23735 NGR_RS07020
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) NGR_RS23730 NGR_RS21555
rocF arginase NGR_RS26545 NGR_RS23830
rocD ornithine aminotransferase NGR_RS26550 NGR_RS06525
PRO3 pyrroline-5-carboxylate reductase NGR_RS22615 NGR_RS21390
put1 proline dehydrogenase NGR_RS11860 NGR_RS21360
putA L-glutamate 5-semialdeyde dehydrogenase NGR_RS11860 NGR_RS21360
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) NGR_RS25770
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase NGR_RS25410
arcB ornithine carbamoyltransferase NGR_RS12140 NGR_RS16730
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 NGR_RS19835 NGR_RS12350
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) NGR_RS19845 NGR_RS12340
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA NGR_RS12355 NGR_RS01720
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) NGR_RS01710 NGR_RS12345
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase NGR_RS12365 NGR_RS22550
aruI 2-ketoarginine decarboxylase NGR_RS12370 NGR_RS07710
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase NGR_RS12135 NGR_RS26550
astD succinylglutamate semialdehyde dehydrogenase NGR_RS27645 NGR_RS23205
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase NGR_RS27475 NGR_RS26100
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 NGR_RS27930 NGR_RS06520
davT 5-aminovalerate aminotransferase NGR_RS06525 NGR_RS12135
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase NGR_RS29675 NGR_RS12210
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase NGR_RS24175 NGR_RS12210
gabD succinate semialdehyde dehydrogenase NGR_RS27930 NGR_RS06520
gabT gamma-aminobutyrate transaminase NGR_RS06525 NGR_RS03045
gbamidase guanidinobutyramidase NGR_RS23790 NGR_RS24455
gbuA guanidinobutyrase NGR_RS23830 NGR_RS01900
gcdG succinyl-CoA:glutarate CoA-transferase NGR_RS06375 NGR_RS02365
gcdH glutaryl-CoA dehydrogenase NGR_RS06370 NGR_RS05525
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase NGR_RS09590 NGR_RS22740
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) NGR_RS06795
ocd ornithine cyclodeaminase NGR_RS09050 NGR_RS03165
odc L-ornithine decarboxylase NGR_RS25770
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) NGR_RS03045 NGR_RS11250
patD gamma-aminobutyraldehyde dehydrogenase NGR_RS22050 NGR_RS26215
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase NGR_RS26225 NGR_RS11875
puo putrescine oxidase
puuA glutamate-putrescine ligase NGR_RS12970 NGR_RS21915
puuB gamma-glutamylputrescine oxidase NGR_RS23860 NGR_RS10555
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase NGR_RS09590 NGR_RS22740
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase NGR_RS25720
rocA 1-pyrroline-5-carboxylate dehydrogenase NGR_RS11860 NGR_RS21360
rocE L-arginine permease NGR_RS11085
speB agmatinase NGR_RS16385 NGR_RS02245

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 Apr 09 2024. 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