GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Acidithiobacillus ferrooxidans ATCC 23270

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
adiA arginine decarboxylase (AdiA/SpeA) AFE_RS06870 AFE_RS00725
aguA agmatine deiminase AFE_RS10035
aguB N-carbamoylputrescine hydrolase AFE_RS11555
patA putrescine aminotransferase (PatA/SpuC) AFE_RS01930 AFE_RS08900
patD gamma-aminobutyraldehyde dehydrogenase AFE_RS08085 AFE_RS09825
gabT gamma-aminobutyrate transaminase AFE_RS08900 AFE_RS01930
gabD succinate semialdehyde dehydrogenase AFE_RS07230 AFE_RS07660
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase
arcB ornithine carbamoyltransferase AFE_RS01925 AFE_RS14025
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
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA AFE_RS00495 AFE_RS02280
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase AFE_RS09345 AFE_RS02230
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase AFE_RS01930 AFE_RS08900
astD succinylglutamate semialdehyde dehydrogenase AFE_RS08085 AFE_RS07230
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase
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)
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) AFE_RS13865 AFE_RS14825
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase AFE_RS07230 AFE_RS09825
davT 5-aminovalerate aminotransferase AFE_RS01930 AFE_RS15145
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AFE_RS10265 AFE_RS03745
gbamidase guanidinobutyramidase AFE_RS11555
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase AFE_RS08085 AFE_RS09825
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
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 AFE_RS01235
puo putrescine oxidase
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase AFE_RS08085 AFE_RS07230
puuA glutamate-putrescine ligase AFE_RS02200
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AFE_RS08085 AFE_RS09825
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase AFE_RS11560
rocA 1-pyrroline-5-carboxylate dehydrogenase AFE_RS08085 AFE_RS07230
rocD ornithine aminotransferase AFE_RS08900 AFE_RS15145
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