GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Maridesulfovibrio zosterae DSM 11974

Best path

rocE, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase H589_RS0117030
rocD ornithine aminotransferase H589_RS0118050 H589_RS0118185
rocA 1-pyrroline-5-carboxylate dehydrogenase H589_RS0107295 H589_RS0109990
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) H589_RS0108255 H589_RS0102990
aguA agmatine deiminase H589_RS0118420
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase H589_RS0114000 H589_RS0102535
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 H589_RS0115910 H589_RS0110285
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) H589_RS0118130 H589_RS0115925
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA H589_RS0115930 H589_RS0110275
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) H589_RS0118130 H589_RS0115925
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase H589_RS0113385
aruI 2-ketoarginine decarboxylase H589_RS0113925
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase H589_RS0113085 H589_RS0118050
astD succinylglutamate semialdehyde dehydrogenase H589_RS0118155 H589_RS0109990
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase
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 H589_RS0101635 H589_RS0112340
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) H589_RS0112345 H589_RS0101630
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) H589_RS0112350 H589_RS0101625
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) H589_RS0112355 H589_RS0101640
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) H589_RS0112360 H589_RS0101620
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase H589_RS0109990 H589_RS0118155
davT 5-aminovalerate aminotransferase H589_RS0118185 H589_RS0104130
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H589_RS0116710
gabD succinate semialdehyde dehydrogenase H589_RS0118155 H589_RS0102680
gabT gamma-aminobutyrate transaminase H589_RS0118185 H589_RS0104130
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase H589_RS0108240
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase H589_RS0109990 H589_RS0107295
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H589_RS0100555
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase H589_RS0102990
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) H589_RS0100395 H589_RS0118050
patD gamma-aminobutyraldehyde dehydrogenase H589_RS0109990 H589_RS0118155
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC H589_RS0116275
prdF proline racemase
PRO3 pyrroline-5-carboxylate reductase H589_RS0113030
puo putrescine oxidase
put1 proline dehydrogenase H589_RS0114955 H589_RS0107295
putA L-glutamate 5-semialdeyde dehydrogenase H589_RS0107295 H589_RS0109990
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase H589_RS0109990 H589_RS0102680
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
speB agmatinase H589_RS0108240

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