GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Lentibacillus jeotgali Grbi

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase ON01_RS00800
rocD ornithine aminotransferase ON01_RS04970 ON01_RS16140
PRO3 pyrroline-5-carboxylate reductase ON01_RS11815
put1 proline dehydrogenase ON01_RS15500
putA L-glutamate 5-semialdeyde dehydrogenase ON01_RS16075 ON01_RS03650
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) ON01_RS11735 ON01_RS01555
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase ON01_RS16960 ON01_RS07805
arcC carbamate kinase ON01_RS06900
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT ON01_RS05295
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) ON01_RS05300 ON01_RS02040
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA ON01_RS05305 ON01_RS02030
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) ON01_RS02040
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase ON01_RS09455
aruI 2-ketoarginine decarboxylase ON01_RS15950
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase ON01_RS06680 ON01_RS04970
astD succinylglutamate semialdehyde dehydrogenase ON01_RS04100 ON01_RS16870
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase ON01_RS13285 ON01_RS06115
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) ON01_RS08915 ON01_RS16055
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase ON01_RS16145 ON01_RS14830
davT 5-aminovalerate aminotransferase ON01_RS14825 ON01_RS16140
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase ON01_RS09200 ON01_RS06105
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase ON01_RS16900 ON01_RS06100
gabD succinate semialdehyde dehydrogenase ON01_RS14830 ON01_RS16145
gabT gamma-aminobutyrate transaminase ON01_RS14825 ON01_RS16140
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase ON01_RS03675 ON01_RS05910
gcdH glutaryl-CoA dehydrogenase ON01_RS03670 ON01_RS13300
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase ON01_RS04100 ON01_RS16395
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) ON01_RS15110 ON01_RS15265
patD gamma-aminobutyraldehyde dehydrogenase ON01_RS04100 ON01_RS16395
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 ON01_RS05550 ON01_RS09045
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase ON01_RS04100 ON01_RS16395
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase ON01_RS16075 ON01_RS03650
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 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