GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Acidovorax caeni R-24608

Best path

artJ, artM, artP, artQ, 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 (36 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 BN2503_RS00930 BN2503_RS00890
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) BN2503_RS00920 BN2503_RS00885
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA BN2503_RS00915 BN2503_RS00880
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) BN2503_RS00925 BN2503_RS00885
rocF arginase BN2503_RS07760
rocD ornithine aminotransferase BN2503_RS03550 BN2503_RS11430
PRO3 pyrroline-5-carboxylate reductase BN2503_RS18030 BN2503_RS19795
put1 proline dehydrogenase BN2503_RS05615
putA L-glutamate 5-semialdeyde dehydrogenase BN2503_RS05615 BN2503_RS03555
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) BN2503_RS13850 BN2503_RS18745
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase BN2503_RS11435 BN2503_RS04795
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 BN2503_RS12960 BN2503_RS02550
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase BN2503_RS11430 BN2503_RS04745
astD succinylglutamate semialdehyde dehydrogenase BN2503_RS02410 BN2503_RS05615
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase BN2503_RS17070 BN2503_RS12305
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 BN2503_RS02255 BN2503_RS06630
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BN2503_RS06735 BN2503_RS02260
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BN2503_RS02265 BN2503_RS06730
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BN2503_RS02270 BN2503_RS09265
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BN2503_RS02275 BN2503_RS06720
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase BN2503_RS02410 BN2503_RS03525
davT 5-aminovalerate aminotransferase BN2503_RS11430 BN2503_RS04745
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BN2503_RS05070 BN2503_RS12155
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BN2503_RS10700 BN2503_RS06880
gabD succinate semialdehyde dehydrogenase BN2503_RS02410 BN2503_RS03525
gabT gamma-aminobutyrate transaminase BN2503_RS03550 BN2503_RS11430
gbamidase guanidinobutyramidase BN2503_RS06240 BN2503_RS02945
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase BN2503_RS01975 BN2503_RS09355
gcdH glutaryl-CoA dehydrogenase BN2503_RS01970 BN2503_RS15695
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase BN2503_RS03525 BN2503_RS02410
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase BN2503_RS13850
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) BN2503_RS03550 BN2503_RS11430
patD gamma-aminobutyraldehyde dehydrogenase BN2503_RS03525 BN2503_RS02410
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
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BN2503_RS03525 BN2503_RS02410
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase BN2503_RS05615 BN2503_RS03555
rocE L-arginine permease BN2503_RS15280 BN2503_RS07220
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