GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Alicycliphilus denitrificans K601

Best path

artJ, artM, artP, artQ, rocF, 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 (41 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 ALIDE2_RS18840 ALIDE2_RS08490
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) ALIDE2_RS18830 ALIDE2_RS08495
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA ALIDE2_RS18825 ALIDE2_RS17660
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) ALIDE2_RS18835 ALIDE2_RS17655
rocF arginase ALIDE2_RS01610
ocd ornithine cyclodeaminase ALIDE2_RS03250
put1 proline dehydrogenase ALIDE2_RS15460
putA L-glutamate 5-semialdeyde dehydrogenase ALIDE2_RS15460 ALIDE2_RS14355
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) ALIDE2_RS15130 ALIDE2_RS04065
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase ALIDE2_RS17555
arcC carbamate kinase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase ALIDE2_RS15675 ALIDE2_RS11230
aruI 2-ketoarginine decarboxylase ALIDE2_RS15150
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase ALIDE2_RS17550 ALIDE2_RS06730
astD succinylglutamate semialdehyde dehydrogenase ALIDE2_RS01490 ALIDE2_RS15600
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase ALIDE2_RS11830 ALIDE2_RS00660
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 ALIDE2_RS06410 ALIDE2_RS18220
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) ALIDE2_RS18330 ALIDE2_RS06405
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) ALIDE2_RS18325 ALIDE2_RS06400
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) ALIDE2_RS06395 ALIDE2_RS20580
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) ALIDE2_RS06390 ALIDE2_RS20585
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase ALIDE2_RS08540 ALIDE2_RS18720
davT 5-aminovalerate aminotransferase ALIDE2_RS17550 ALIDE2_RS06730
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase ALIDE2_RS08370 ALIDE2_RS05800
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase ALIDE2_RS03170 ALIDE2_RS20405
gabD succinate semialdehyde dehydrogenase ALIDE2_RS18720 ALIDE2_RS08540
gabT gamma-aminobutyrate transaminase ALIDE2_RS23265 ALIDE2_RS17550
gbamidase guanidinobutyramidase ALIDE2_RS22725
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase ALIDE2_RS09305 ALIDE2_RS17345
gcdH glutaryl-CoA dehydrogenase ALIDE2_RS17340 ALIDE2_RS20710
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase ALIDE2_RS07695 ALIDE2_RS07670
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) ALIDE2_RS11990
odc L-ornithine decarboxylase ALIDE2_RS15130
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) ALIDE2_RS23265 ALIDE2_RS17550
patD gamma-aminobutyraldehyde dehydrogenase ALIDE2_RS07695 ALIDE2_RS07670
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 ALIDE2_RS21670
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase ALIDE2_RS17665
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase ALIDE2_RS07695 ALIDE2_RS07670
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase ALIDE2_RS22385
rocA 1-pyrroline-5-carboxylate dehydrogenase ALIDE2_RS15460 ALIDE2_RS14355
rocD ornithine aminotransferase ALIDE2_RS17550 ALIDE2_RS06730
rocE L-arginine permease ALIDE2_RS12155
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