GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Haloglycomyces albus DSM 45210

Best path

rocE, arcA, arcB, arcC, ocd, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
arcA arginine deiminase HALAL_RS0106630
arcB ornithine carbamoyltransferase HALAL_RS0112705 HALAL_RS0114950
arcC carbamate kinase
ocd ornithine cyclodeaminase
put1 proline dehydrogenase HALAL_RS0107260
putA L-glutamate 5-semialdeyde dehydrogenase HALAL_RS0103000 HALAL_RS0112015
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
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) HALAL_RS0113975 HALAL_RS0102765
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA HALAL_RS0102760 HALAL_RS0113980
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) HALAL_RS0102765 HALAL_RS0104120
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase
aruI 2-ketoarginine decarboxylase HALAL_RS0110735 HALAL_RS0114685
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase HALAL_RS0112700 HALAL_RS0102620
astD succinylglutamate semialdehyde dehydrogenase HALAL_RS0112015 HALAL_RS0110770
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase HALAL_RS0107190 HALAL_RS0108855
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) HALAL_RS0101160
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) HALAL_RS0101165 HALAL_RS0101170
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) HALAL_RS0101170 HALAL_RS0101415
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase HALAL_RS0102625 HALAL_RS0112015
davT 5-aminovalerate aminotransferase HALAL_RS0102620 HALAL_RS0112700
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HALAL_RS0110635
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HALAL_RS0108355 HALAL_RS0110635
gabD succinate semialdehyde dehydrogenase HALAL_RS0102625 HALAL_RS0110770
gabT gamma-aminobutyrate transaminase HALAL_RS0102620 HALAL_RS0113645
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase HALAL_RS0107635 HALAL_RS0104340
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase HALAL_RS0112015 HALAL_RS0110770
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
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) HALAL_RS0112700 HALAL_RS0102620
patD gamma-aminobutyraldehyde dehydrogenase HALAL_RS0112015 HALAL_RS0110770
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
puo putrescine oxidase
puuA glutamate-putrescine ligase HALAL_RS0111445
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase HALAL_RS0112015 HALAL_RS0110770
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase HALAL_RS0103000 HALAL_RS0112015
rocD ornithine aminotransferase HALAL_RS0102620 HALAL_RS0113645
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