GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Amycolatopsis halophila YIM 93223

Best path

rocE, arg-monooxygenase, gbamidase, kauB, gbuA, 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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
arg-monooxygenase arginine 2-monooxygenase AMYHA_RS23880
gbamidase guanidinobutyramidase AMYHA_RS23875
kauB 4-guanidinobutyraldehyde dehydrogenase AMYHA_RS12585 AMYHA_RS25345
gbuA guanidinobutyrase AMYHA_RS23885
gabT gamma-aminobutyrate transaminase AMYHA_RS13090 AMYHA_RS09750
gabD succinate semialdehyde dehydrogenase AMYHA_RS09755 AMYHA_RS16465
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) AMYHA_RS05040
aguA agmatine deiminase AMYHA_RS23905
aguB N-carbamoylputrescine hydrolase AMYHA_RS23910
arcA arginine deiminase AMYHA_RS02430
arcB ornithine carbamoyltransferase AMYHA_RS15985 AMYHA_RS11270
arcC carbamate kinase
aroD L-arginine oxidase
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT AMYHA_RS03540
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) AMYHA_RS03535 AMYHA_RS18270
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA AMYHA_RS03530 AMYHA_RS18260
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) AMYHA_RS03535 AMYHA_RS22135
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase AMYHA_RS01030 AMYHA_RS01585
aruI 2-ketoarginine decarboxylase AMYHA_RS20650 AMYHA_RS20285
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase AMYHA_RS15990 AMYHA_RS17620
astD succinylglutamate semialdehyde dehydrogenase AMYHA_RS13095 AMYHA_RS08895
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase AMYHA_RS06490 AMYHA_RS10330
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) AMYHA_RS16255 AMYHA_RS04370
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AMYHA_RS10525 AMYHA_RS20915
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) AMYHA_RS05545 AMYHA_RS10540
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) AMYHA_RS20895 AMYHA_RS10515
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase AMYHA_RS09755 AMYHA_RS13095
davT 5-aminovalerate aminotransferase AMYHA_RS07330 AMYHA_RS09750
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AMYHA_RS20710 AMYHA_RS24905
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AMYHA_RS03760 AMYHA_RS17210
gcdG succinyl-CoA:glutarate CoA-transferase AMYHA_RS12685 AMYHA_RS16450
gcdH glutaryl-CoA dehydrogenase AMYHA_RS24060 AMYHA_RS09585
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) AMYHA_RS02030
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) AMYHA_RS13090 AMYHA_RS15990
patD gamma-aminobutyraldehyde dehydrogenase AMYHA_RS23925 AMYHA_RS20335
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 AMYHA_RS01435
puo putrescine oxidase AMYHA_RS13775 AMYHA_RS23045
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase AMYHA_RS10060 AMYHA_RS09435
puuA glutamate-putrescine ligase AMYHA_RS20005 AMYHA_RS24480
puuB gamma-glutamylputrescine oxidase AMYHA_RS23075
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AMYHA_RS13095 AMYHA_RS08895
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase AMYHA_RS20010 AMYHA_RS23110
rocA 1-pyrroline-5-carboxylate dehydrogenase AMYHA_RS09435 AMYHA_RS10060
rocD ornithine aminotransferase AMYHA_RS17620 AMYHA_RS15990
rocF arginase AMYHA_RS23885 AMYHA_RS17685
speB agmatinase AMYHA_RS23885

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