GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Neptunomonas antarctica S3-22

Best path

artJ, artM, artP, artQ, arcA, arcB, arcC, 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 (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 Nant_RS15240 Nant_RS20475
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) Nant_RS15250 Nant_RS15245
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Nant_RS15235 Nant_RS03650
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) Nant_RS15245 Nant_RS15250
arcA arginine deiminase Nant_RS13745
arcB ornithine carbamoyltransferase Nant_RS13740 Nant_RS02915
arcC carbamate kinase Nant_RS13735
rocD ornithine aminotransferase Nant_RS02920 Nant_RS20480
PRO3 pyrroline-5-carboxylate reductase Nant_RS15955
put1 proline dehydrogenase Nant_RS16405 Nant_RS11275
putA L-glutamate 5-semialdeyde dehydrogenase Nant_RS16405 Nant_RS17555
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) Nant_RS19750
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) Nant_RS20570 Nant_RS20565
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) Nant_RS20565 Nant_RS20570
aruH L-arginine:pyruvate transaminase Nant_RS03730 Nant_RS07615
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase Nant_RS20565 Nant_RS20570
astB N-succinylarginine dihydrolase Nant_RS20555
astC succinylornithine transaminase Nant_RS20605 Nant_RS02920
astD succinylglutamate semialdehyde dehydrogenase Nant_RS20560 Nant_RS12190
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase Nant_RS07655 Nant_RS01890
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 Nant_RS08260
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Nant_RS08265 Nant_RS12655
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Nant_RS08270
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Nant_RS08275 Nant_RS10025
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Nant_RS08280 Nant_RS10030
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase Nant_RS11485 Nant_RS18090
davT 5-aminovalerate aminotransferase Nant_RS20605 Nant_RS20480
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Nant_RS13960 Nant_RS07340
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Nant_RS08070 Nant_RS07350
gabD succinate semialdehyde dehydrogenase Nant_RS11485 Nant_RS18090
gabT gamma-aminobutyrate transaminase Nant_RS18095 Nant_RS17935
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase Nant_RS17905
gcdG succinyl-CoA:glutarate CoA-transferase Nant_RS10240 Nant_RS06935
gcdH glutaryl-CoA dehydrogenase Nant_RS10235 Nant_RS12630
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) Nant_RS19765
kauB 4-guanidinobutyraldehyde dehydrogenase Nant_RS17925 Nant_RS19705
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) Nant_RS19760
ocd ornithine cyclodeaminase Nant_RS05745
odc L-ornithine decarboxylase Nant_RS07100
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) Nant_RS17935 Nant_RS07910
patD gamma-aminobutyraldehyde dehydrogenase Nant_RS17925 Nant_RS19705
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 Nant_RS18000 Nant_RS17945
puuB gamma-glutamylputrescine oxidase Nant_RS18055 Nant_RS18005
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Nant_RS17925 Nant_RS19705
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase Nant_RS16405 Nant_RS17555
rocE L-arginine permease
rocF arginase Nant_RS17905
speB agmatinase Nant_RS17905

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.

Links

Downloads

Related tools

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