GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Limnohabitans curvus MWH-C5

Best path

braC, braD, braE, braF, braG, rocF, rocD, rocA

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
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC B9Z44_RS00730
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) B9Z44_RS04225 B9Z44_RS10015
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) B9Z44_RS04220 B9Z44_RS12865
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) B9Z44_RS05725 B9Z44_RS04215
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) B9Z44_RS05720 B9Z44_RS04210
rocF arginase
rocD ornithine aminotransferase B9Z44_RS03080
rocA 1-pyrroline-5-carboxylate dehydrogenase B9Z44_RS11550 B9Z44_RS07890
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) B9Z44_RS00360
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase B9Z44_RS03085 B9Z44_RS03805
arcC carbamate kinase
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)
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA B9Z44_RS09155 B9Z44_RS03630
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) B9Z44_RS09150
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase B9Z44_RS01960 B9Z44_RS00765
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase B9Z44_RS03080
astD succinylglutamate semialdehyde dehydrogenase B9Z44_RS07890 B9Z44_RS11745
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase B9Z44_RS11030 B9Z44_RS12465
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase B9Z44_RS11745 B9Z44_RS01610
davT 5-aminovalerate aminotransferase B9Z44_RS03080 B9Z44_RS03845
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase B9Z44_RS10090 B9Z44_RS01330
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase B9Z44_RS01305 B9Z44_RS14295
gabD succinate semialdehyde dehydrogenase B9Z44_RS01610 B9Z44_RS11745
gabT gamma-aminobutyrate transaminase B9Z44_RS03080 B9Z44_RS03845
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase B9Z44_RS06760 B9Z44_RS01590
gcdH glutaryl-CoA dehydrogenase B9Z44_RS01320 B9Z44_RS14300
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase B9Z44_RS11550 B9Z44_RS11745
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) B9Z44_RS13415
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase B9Z44_RS00360
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) B9Z44_RS03080
patD gamma-aminobutyraldehyde dehydrogenase B9Z44_RS11550 B9Z44_RS11745
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 B9Z44_RS08295
puo putrescine oxidase
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase B9Z44_RS11550 B9Z44_RS07890
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase B9Z44_RS11550 B9Z44_RS09990
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocE L-arginine permease B9Z44_RS14795
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