GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Frankia alni ACN14a

Best path

rocE, adiA, aguA, aguB, patA, patD, gabT, gabD

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase FRAAL_RS00755
aguB N-carbamoylputrescine hydrolase FRAAL_RS06160 FRAAL_RS00760
patA putrescine aminotransferase (PatA/SpuC) FRAAL_RS22695 FRAAL_RS06200
patD gamma-aminobutyraldehyde dehydrogenase FRAAL_RS26230 FRAAL_RS00920
gabT gamma-aminobutyrate transaminase FRAAL_RS26530 FRAAL_RS06200
gabD succinate semialdehyde dehydrogenase FRAAL_RS27755 FRAAL_RS00920
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase
arcB ornithine carbamoyltransferase FRAAL_RS22690 FRAAL_RS22855
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 FRAAL_RS26080
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) FRAAL_RS26085 FRAAL_RS10415
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA FRAAL_RS26090 FRAAL_RS24880
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) FRAAL_RS26085 FRAAL_RS10415
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase FRAAL_RS26455 FRAAL_RS04605
aruI 2-ketoarginine decarboxylase FRAAL_RS25490 FRAAL_RS07770
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase FRAAL_RS22695 FRAAL_RS26530
astD succinylglutamate semialdehyde dehydrogenase FRAAL_RS18340 FRAAL_RS22990
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase FRAAL_RS21530 FRAAL_RS23880
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) FRAAL_RS03125
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) FRAAL_RS03130
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) FRAAL_RS03135 FRAAL_RS16765
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) FRAAL_RS03140 FRAAL_RS21210
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase FRAAL_RS14890 FRAAL_RS18340
davT 5-aminovalerate aminotransferase FRAAL_RS26530 FRAAL_RS06200
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase FRAAL_RS25610 FRAAL_RS13585
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase FRAAL_RS08595 FRAAL_RS20845
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase FRAAL_RS20775 FRAAL_RS14895
gcdH glutaryl-CoA dehydrogenase FRAAL_RS13805 FRAAL_RS12160
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase FRAAL_RS00920 FRAAL_RS07200
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) FRAAL_RS19800 FRAAL_RS13625
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase
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
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
PRO3 pyrroline-5-carboxylate reductase FRAAL_RS04180
puo putrescine oxidase
put1 proline dehydrogenase FRAAL_RS18995 FRAAL_RS08175
putA L-glutamate 5-semialdeyde dehydrogenase FRAAL_RS18990 FRAAL_RS00920
puuA glutamate-putrescine ligase FRAAL_RS22525 FRAAL_RS28045
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase FRAAL_RS00920 FRAAL_RS14890
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase FRAAL_RS18990 FRAAL_RS00920
rocD ornithine aminotransferase FRAAL_RS26530 FRAAL_RS06200
rocF arginase
speB agmatinase

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