GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Novosphingobium aromaticivorans DSM 12444

Best path

rocE, adiA, aguA, aguB, patA, patD, 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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase SARO_RS16015
aguB N-carbamoylputrescine hydrolase SARO_RS15710
patA putrescine aminotransferase (PatA/SpuC) SARO_RS14875 SARO_RS15955
patD gamma-aminobutyraldehyde dehydrogenase SARO_RS14550 SARO_RS19930
gabT gamma-aminobutyrate transaminase SARO_RS14875 SARO_RS13120
gabD succinate semialdehyde dehydrogenase SARO_RS13125 SARO_RS03980
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase
arcB ornithine carbamoyltransferase SARO_RS15950 SARO_RS15545
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 SARO_RS05745 SARO_RS18790
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) SARO_RS04420
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) SARO_RS04420
aruH L-arginine:pyruvate transaminase SARO_RS02235 SARO_RS02510
aruI 2-ketoarginine decarboxylase SARO_RS11375
astA arginine N-succinyltransferase SARO_RS04420
astB N-succinylarginine dihydrolase SARO_RS04415
astC succinylornithine transaminase SARO_RS15955 SARO_RS13120
astD succinylglutamate semialdehyde dehydrogenase SARO_RS04690 SARO_RS17080
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase SARO_RS04040 SARO_RS05335
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) SARO_RS01485 SARO_RS05165
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) SARO_RS01485 SARO_RS14425
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase SARO_RS17165 SARO_RS14885
davT 5-aminovalerate aminotransferase SARO_RS13120 SARO_RS15955
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SARO_RS04305 SARO_RS07105
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SARO_RS02760 SARO_RS18115
gbamidase guanidinobutyramidase SARO_RS15710
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase SARO_RS18980 SARO_RS17240
gcdH glutaryl-CoA dehydrogenase SARO_RS17970 SARO_RS08250
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase SARO_RS14895 SARO_RS14550
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
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 SARO_RS05695
puo putrescine oxidase
put1 proline dehydrogenase SARO_RS03520 SARO_RS14900
putA L-glutamate 5-semialdeyde dehydrogenase SARO_RS03520 SARO_RS14550
puuA glutamate-putrescine ligase SARO_RS13155
puuB gamma-glutamylputrescine oxidase SARO_RS14935 SARO_RS01270
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase SARO_RS14895 SARO_RS14550
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase SARO_RS03520 SARO_RS14550
rocD ornithine aminotransferase SARO_RS13120 SARO_RS14875
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