GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Paraburkholderia phymatum STM815

Best path

artJ, artM, artP, artQ, arcA, arcB, arcC, odc, puuA, puuB, puuC, puuD, 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 (52 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT BPHY_RS09055 BPHY_RS17400
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) BPHY_RS09105 BPHY_RS37110
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA BPHY_RS09100 BPHY_RS37105
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) BPHY_RS09110 BPHY_RS11015
arcA arginine deiminase BPHY_RS05530 BPHY_RS32080
arcB ornithine carbamoyltransferase BPHY_RS32075 BPHY_RS02660
arcC carbamate kinase BPHY_RS32070
odc L-ornithine decarboxylase BPHY_RS32090 BPHY_RS11130
puuA glutamate-putrescine ligase BPHY_RS18060 BPHY_RS38400
puuB gamma-glutamylputrescine oxidase BPHY_RS18185 BPHY_RS32820
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BPHY_RS18040 BPHY_RS34150
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase BPHY_RS18055 BPHY_RS34660
gabT gamma-aminobutyrate transaminase BPHY_RS18065 BPHY_RS23215
gabD succinate semialdehyde dehydrogenase BPHY_RS27205 BPHY_RS24330
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) BPHY_RS32100 BPHY_RS11130
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arg-monooxygenase arginine 2-monooxygenase BPHY_RS38325
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) BPHY_RS09085 BPHY_RS09080
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) BPHY_RS09080 BPHY_RS09085
aruH L-arginine:pyruvate transaminase BPHY_RS32600 BPHY_RS03085
aruI 2-ketoarginine decarboxylase BPHY_RS37050 BPHY_RS30940
astA arginine N-succinyltransferase BPHY_RS09085 BPHY_RS09080
astB N-succinylarginine dihydrolase BPHY_RS09070
astC succinylornithine transaminase BPHY_RS09090 BPHY_RS02980
astD succinylglutamate semialdehyde dehydrogenase BPHY_RS09075 BPHY_RS19265
astE succinylglutamate desuccinylase BPHY_RS09065
atoB acetyl-CoA C-acetyltransferase BPHY_RS04915 BPHY_RS04940
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 BPHY_RS15375 BPHY_RS02950
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BPHY_RS02955 BPHY_RS11455
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BPHY_RS02960
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BPHY_RS02965 BPHY_RS15490
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BPHY_RS02970 BPHY_RS15485
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 BPHY_RS00475
davD glutarate semialdehyde dehydrogenase BPHY_RS24330 BPHY_RS16380
davT 5-aminovalerate aminotransferase BPHY_RS24335 BPHY_RS23215
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BPHY_RS13655 BPHY_RS24290
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BPHY_RS01920 BPHY_RS35840
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase BPHY_RS03195 BPHY_RS30365
gcdG succinyl-CoA:glutarate CoA-transferase BPHY_RS08225 BPHY_RS31935
gcdH glutaryl-CoA dehydrogenase BPHY_RS12365 BPHY_RS18015
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase BPHY_RS18040 BPHY_RS34150
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) BPHY_RS00525
ocd ornithine cyclodeaminase
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) BPHY_RS18065 BPHY_RS32700
patD gamma-aminobutyraldehyde dehydrogenase BPHY_RS18040 BPHY_RS16780
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase BPHY_RS16950 BPHY_RS23455
PRO3 pyrroline-5-carboxylate reductase BPHY_RS12780
puo putrescine oxidase
put1 proline dehydrogenase BPHY_RS15380 BPHY_RS29565
putA L-glutamate 5-semialdeyde dehydrogenase BPHY_RS15380 BPHY_RS23615
rocA 1-pyrroline-5-carboxylate dehydrogenase BPHY_RS15380 BPHY_RS23615
rocD ornithine aminotransferase BPHY_RS24335 BPHY_RS23215
rocE L-arginine permease BPHY_RS03010 BPHY_RS31005
rocF arginase BPHY_RS30365 BPHY_RS03195
speB agmatinase BPHY_RS03195 BPHY_RS30365

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