GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Thermoactinomyces daqus H-18

Best path

rocE, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease JG50_RS0105800 JG50_RS0115245
rocF arginase JG50_RS0115295 JG50_RS0107325
rocD ornithine aminotransferase JG50_RS0114245 JG50_RS0106665
PRO3 pyrroline-5-carboxylate reductase JG50_RS0111965
put1 proline dehydrogenase JG50_RS0105265
putA L-glutamate 5-semialdeyde dehydrogenase JG50_RS0105270 JG50_RS0103810
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) JG50_RS0105990 JG50_RS0108660
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase JG50_RS0106660 JG50_RS0106315
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 JG50_RS0106740 JG50_RS0104005
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) JG50_RS0106735 JG50_RS0104010
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA JG50_RS0106730 JG50_RS0104015
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) JG50_RS0100595 JG50_RS0106735
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase JG50_RS0113075 JG50_RS0114340
aruI 2-ketoarginine decarboxylase JG50_RS0111070 JG50_RS0106835
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase JG50_RS0106665 JG50_RS0102760
astD succinylglutamate semialdehyde dehydrogenase JG50_RS0104290 JG50_RS0117670
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase JG50_RS0107240 JG50_RS0101445
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) JG50_RS0105535 JG50_RS0108245
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 JG50_RS0106450 JG50_RS0102490
davD glutarate semialdehyde dehydrogenase JG50_RS0104290 JG50_RS0109305
davT 5-aminovalerate aminotransferase JG50_RS0110325 JG50_RS0106665
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase JG50_RS0105825 JG50_RS0106695
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase JG50_RS0105235 JG50_RS0113065
gabD succinate semialdehyde dehydrogenase JG50_RS0104290 JG50_RS0103810
gabT gamma-aminobutyrate transaminase JG50_RS0105185 JG50_RS0110325
gbamidase guanidinobutyramidase JG50_RS0114345
gbuA guanidinobutyrase JG50_RS0107325
gcdG succinyl-CoA:glutarate CoA-transferase JG50_RS0101450 JG50_RS0109910
gcdH glutaryl-CoA dehydrogenase JG50_RS0107230 JG50_RS0113945
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase JG50_RS0103810 JG50_RS0109305
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
patA putrescine aminotransferase (PatA/SpuC) JG50_RS0114245 JG50_RS0105185
patD gamma-aminobutyraldehyde dehydrogenase JG50_RS0103810 JG50_RS0109305
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase JG50_RS0103810 JG50_RS0109305
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase JG50_RS0113670
rocA 1-pyrroline-5-carboxylate dehydrogenase JG50_RS0105270 JG50_RS0103810
speB agmatinase JG50_RS0107325

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