GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Sedimenticola selenatireducens DSM 17993

Best path

artJ, artM, artP, artQ, rocF, ocd, 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 (41 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 A3GO_RS0106840
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) A3GO_RS0106830 A3GO_RS0106835
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA A3GO_RS0106845 A3GO_RS0104265
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) A3GO_RS0106835 A3GO_RS0106830
rocF arginase A3GO_RS24575
ocd ornithine cyclodeaminase A3GO_RS0118915
put1 proline dehydrogenase A3GO_RS0114220
putA L-glutamate 5-semialdeyde dehydrogenase A3GO_RS0114220 A3GO_RS0120300
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) A3GO_RS0112475
aguA agmatine deiminase A3GO_RS0113295
aguB N-carbamoylputrescine hydrolase A3GO_RS0113290
arcA arginine deiminase
arcB ornithine carbamoyltransferase A3GO_RS0110385 A3GO_RS23545
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 A3GO_RS0105215 A3GO_RS0105540
aruI 2-ketoarginine decarboxylase A3GO_RS0114660
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase A3GO_RS0110380 A3GO_RS0108935
astD succinylglutamate semialdehyde dehydrogenase A3GO_RS0110905 A3GO_RS0115130
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase A3GO_RS0108835 A3GO_RS0107785
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 A3GO_RS0114190 A3GO_RS0114160
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) A3GO_RS0114215 A3GO_RS0114165
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) A3GO_RS0114210 A3GO_RS0114170
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) A3GO_RS0114175 A3GO_RS0114425
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) A3GO_RS0114200 A3GO_RS0114180
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase A3GO_RS0115130 A3GO_RS0114560
davT 5-aminovalerate aminotransferase A3GO_RS0110380 A3GO_RS0109800
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase A3GO_RS0114405 A3GO_RS0115400
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase A3GO_RS0108695 A3GO_RS0114400
gabD succinate semialdehyde dehydrogenase A3GO_RS0115130 A3GO_RS0115615
gabT gamma-aminobutyrate transaminase A3GO_RS0108935 A3GO_RS0110520
gbamidase guanidinobutyramidase A3GO_RS0113290
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase A3GO_RS0109000 A3GO_RS0114455
gcdH glutaryl-CoA dehydrogenase A3GO_RS0115815 A3GO_RS0114380
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase A3GO_RS0114560 A3GO_RS0115130
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) A3GO_RS0115115
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) A3GO_RS0110380 A3GO_RS0108935
patD gamma-aminobutyraldehyde dehydrogenase A3GO_RS0117140 A3GO_RS0115130
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 A3GO_RS0110650
puo putrescine oxidase
puuA glutamate-putrescine ligase A3GO_RS0103225
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase A3GO_RS0114560 A3GO_RS0117140
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase A3GO_RS0105635
rocA 1-pyrroline-5-carboxylate dehydrogenase A3GO_RS0114220 A3GO_RS0120300
rocD ornithine aminotransferase A3GO_RS0110380 A3GO_RS0108935
rocE L-arginine permease
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