GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Stutzerimonas stutzeri A1501

Best path

artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD

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 (43 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 PST_RS20435 PST_RS11840
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) PST_RS20445 PST_RS11845
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA PST_RS20430 PST_RS00075
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) PST_RS20440 PST_RS11845
adiA arginine decarboxylase (AdiA/SpeA) PST_RS04995 PST_RS11335
aguA agmatine deiminase PST_RS00310
aguB N-carbamoylputrescine hydrolase PST_RS00315
puuA glutamate-putrescine ligase PST_RS00325 PST_RS00335
puuB gamma-glutamylputrescine oxidase PST_RS11935 PST_RS02480
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PST_RS00240 PST_RS08835
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase PST_RS00330
gabT gamma-aminobutyrate transaminase PST_RS00340 PST_RS03780
gabD succinate semialdehyde dehydrogenase PST_RS00500 PST_RS03775
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase PST_RS03490 PST_RS19800
arcB ornithine carbamoyltransferase PST_RS03485 PST_RS19805
arcC carbamate kinase PST_RS03480 PST_RS19810
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 PST_RS15170 PST_RS16510
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase PST_RS08350 PST_RS03780
astD succinylglutamate semialdehyde dehydrogenase PST_RS00240 PST_RS03775
astE succinylglutamate desuccinylase PST_RS08360
atoB acetyl-CoA C-acetyltransferase PST_RS03530 PST_RS16155
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 PST_RS14950
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) PST_RS14955 PST_RS16080
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) PST_RS14960
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) PST_RS14965 PST_RS02170
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PST_RS14970 PST_RS18540
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase PST_RS00500 PST_RS03775
davT 5-aminovalerate aminotransferase PST_RS03780 PST_RS08350
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PST_RS09740 PST_RS06175
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PST_RS08735 PST_RS00510
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase PST_RS02290 PST_RS08605
gcdH glutaryl-CoA dehydrogenase PST_RS02285 PST_RS09725
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase PST_RS00240 PST_RS08835
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) PST_RS19980
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase PST_RS05085 PST_RS11335
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) PST_RS00340 PST_RS00235
patD gamma-aminobutyraldehyde dehydrogenase PST_RS00240 PST_RS08835
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 PST_RS19745
puo putrescine oxidase
put1 proline dehydrogenase PST_RS06320
putA L-glutamate 5-semialdeyde dehydrogenase PST_RS06320 PST_RS00500
rocA 1-pyrroline-5-carboxylate dehydrogenase PST_RS06320 PST_RS00500
rocD ornithine aminotransferase PST_RS03780 PST_RS08350
rocE L-arginine permease PST_RS13100
rocF arginase
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