GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Rhodanobacter denitrificans FW104-10B01

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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease LRK54_RS02890 LRK54_RS15610
rocF arginase LRK54_RS05930 LRK54_RS15360
rocD ornithine aminotransferase LRK54_RS04500 LRK54_RS03035
PRO3 pyrroline-5-carboxylate reductase LRK54_RS04260
put1 proline dehydrogenase LRK54_RS07135
putA L-glutamate 5-semialdeyde dehydrogenase LRK54_RS07135 LRK54_RS04485
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) LRK54_RS09140
aguA agmatine deiminase LRK54_RS00335
aguB N-carbamoylputrescine hydrolase LRK54_RS00340
arcA arginine deiminase
arcB ornithine carbamoyltransferase LRK54_RS02415 LRK54_RS04220
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 LRK54_RS14735 LRK54_RS16245
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase LRK54_RS11155 LRK54_RS00830
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase LRK54_RS06590 LRK54_RS04500
astD succinylglutamate semialdehyde dehydrogenase LRK54_RS02575 LRK54_RS04485
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase LRK54_RS15265 LRK54_RS00050
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) LRK54_RS10835 LRK54_RS03155
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) LRK54_RS12880 LRK54_RS14195
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 LRK54_RS10455 LRK54_RS12060
davD glutarate semialdehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
davT 5-aminovalerate aminotransferase LRK54_RS04500 LRK54_RS06590
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase LRK54_RS15165 LRK54_RS16925
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase LRK54_RS00055 LRK54_RS16925
gabD succinate semialdehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
gabT gamma-aminobutyrate transaminase LRK54_RS04500 LRK54_RS04150
gbamidase guanidinobutyramidase LRK54_RS00340
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase LRK54_RS07425
gcdH glutaryl-CoA dehydrogenase LRK54_RS02070 LRK54_RS02105
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
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) LRK54_RS04500 LRK54_RS04150
patD gamma-aminobutyraldehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
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 LRK54_RS08105
puuB gamma-glutamylputrescine oxidase LRK54_RS18070
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase LRK54_RS07135 LRK54_RS04485
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