GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Rhizobium etli CFN 42

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 (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 RHE_RS16985 RHE_RS15140
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) RHE_RS17010 RHE_RS16960
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) RHE_RS17005
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) RHE_RS17000 RHE_RS25470
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) RHE_RS16995 RHE_RS25475
rocF arginase RHE_RS19700 RHE_RS10965
rocD ornithine aminotransferase RHE_RS19705 RHE_RS00475
PRO3 pyrroline-5-carboxylate reductase RHE_RS15425 RHE_RS28560
put1 proline dehydrogenase RHE_RS28430 RHE_RS00450
putA L-glutamate 5-semialdeyde dehydrogenase RHE_RS28430 RHE_RS16180
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase RHE_RS02615 RHE_RS08405
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 RHE_RS12350 RHE_RS23645
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) RHE_RS30300 RHE_RS10950
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA RHE_RS23640 RHE_RS10945
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) RHE_RS23650 RHE_RS30305
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase RHE_RS23780 RHE_RS15340
aruI 2-ketoarginine decarboxylase RHE_RS27855
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase RHE_RS02610 RHE_RS19705
astD succinylglutamate semialdehyde dehydrogenase RHE_RS28200 RHE_RS16180
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase RHE_RS20545 RHE_RS23190
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 RHE_RS23010 RHE_RS00470
davT 5-aminovalerate aminotransferase RHE_RS00475 RHE_RS02610
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RHE_RS01800 RHE_RS02825
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RHE_RS02825 RHE_RS19395
gabD succinate semialdehyde dehydrogenase RHE_RS23010 RHE_RS00470
gabT gamma-aminobutyrate transaminase RHE_RS00475 RHE_RS10975
gbamidase guanidinobutyramidase RHE_RS12110
gbuA guanidinobutyrase RHE_RS10965 RHE_RS08005
gcdG succinyl-CoA:glutarate CoA-transferase RHE_RS14710
gcdH glutaryl-CoA dehydrogenase RHE_RS25445 RHE_RS23195
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase RHE_RS28500 RHE_RS19035
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase RHE_RS00300
odc L-ornithine decarboxylase RHE_RS18555
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) RHE_RS06730 RHE_RS28245
patD gamma-aminobutyraldehyde dehydrogenase RHE_RS18735 RHE_RS05810
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase RHE_RS28470 RHE_RS02295
puo putrescine oxidase
puuA glutamate-putrescine ligase RHE_RS03570 RHE_RS06725
puuB gamma-glutamylputrescine oxidase RHE_RS03565 RHE_RS28205
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase RHE_RS28500 RHE_RS19035
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase RHE_RS18510
rocA 1-pyrroline-5-carboxylate dehydrogenase RHE_RS28430 RHE_RS16180
rocE L-arginine permease RHE_RS25845
speB agmatinase RHE_RS08005 RHE_RS10965

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