GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Halomonas xinjiangensis TRM 0175

Best path

artJ, artM, artP, artQ, adiA, aguA, aguB, 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 (47 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 JH15_RS09820 JH15_RS16050
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) JH15_RS09825 JH15_RS16060
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA JH15_RS09835 JH15_RS16045
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) JH15_RS09830 JH15_RS16055
adiA arginine decarboxylase (AdiA/SpeA) JH15_RS07315
aguA agmatine deiminase JH15_RS08540 JH15_RS02680
aguB N-carbamoylputrescine hydrolase JH15_RS02685
puuA glutamate-putrescine ligase JH15_RS03070 JH15_RS03050
puuB gamma-glutamylputrescine oxidase JH15_RS03060 JH15_RS03095
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase JH15_RS03035 JH15_RS03240
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase JH15_RS03045 JH15_RS10440
gabT gamma-aminobutyrate transaminase JH15_RS03040 JH15_RS04225
gabD succinate semialdehyde dehydrogenase JH15_RS15380 JH15_RS16505
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase
arcB ornithine carbamoyltransferase JH15_RS01910 JH15_RS13095
arcC carbamate kinase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) JH15_RS09235 JH15_RS09240
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) JH15_RS09240 JH15_RS09235
aruH L-arginine:pyruvate transaminase JH15_RS16040 JH15_RS12295
aruI 2-ketoarginine decarboxylase JH15_RS16030
astA arginine N-succinyltransferase JH15_RS09240 JH15_RS09235
astB N-succinylarginine dihydrolase JH15_RS09250
astC succinylornithine transaminase JH15_RS09230 JH15_RS04225
astD succinylglutamate semialdehyde dehydrogenase JH15_RS09245 JH15_RS03035
astE succinylglutamate desuccinylase JH15_RS09840
atoB acetyl-CoA C-acetyltransferase JH15_RS12340 JH15_RS03630
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) JH15_RS14385
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) JH15_RS09320 JH15_RS14395
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) JH15_RS09325 JH15_RS16670
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase JH15_RS15380 JH15_RS16505
davT 5-aminovalerate aminotransferase JH15_RS04225 JH15_RS09230
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase JH15_RS10685 JH15_RS15755
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase JH15_RS16995 JH15_RS10680
gbamidase guanidinobutyramidase JH15_RS02685
gbuA guanidinobutyrase JH15_RS15565
gcdG succinyl-CoA:glutarate CoA-transferase JH15_RS01440 JH15_RS15320
gcdH glutaryl-CoA dehydrogenase JH15_RS01445 JH15_RS02120
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase JH15_RS03035 JH15_RS03240
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) JH15_RS01050
ocd ornithine cyclodeaminase JH15_RS05015
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
patA putrescine aminotransferase (PatA/SpuC) JH15_RS03040 JH15_RS05025
patD gamma-aminobutyraldehyde dehydrogenase JH15_RS03035 JH15_RS03240
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 JH15_RS12260
puo putrescine oxidase
put1 proline dehydrogenase JH15_RS11260
putA L-glutamate 5-semialdeyde dehydrogenase JH15_RS11260 JH15_RS05310
rocA 1-pyrroline-5-carboxylate dehydrogenase JH15_RS11260 JH15_RS05310
rocD ornithine aminotransferase JH15_RS04225 JH15_RS03040
rocE L-arginine permease
rocF arginase JH15_RS15565
speB agmatinase JH15_RS15565

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 Sep 24 2021. 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