GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Novosphingobium barchaimii LL02

Best path

rocE, astA, astB, astC, astD, astE

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
astA arginine N-succinyltransferase V474_RS11830
astB N-succinylarginine dihydrolase V474_RS11835
astC succinylornithine transaminase V474_RS13815 V474_RS23835
astD succinylglutamate semialdehyde dehydrogenase V474_RS11820 V474_RS12660
astE succinylglutamate desuccinylase
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase V474_RS14225
aguB N-carbamoylputrescine hydrolase V474_RS06790
arcA arginine deiminase
arcB ornithine carbamoyltransferase V474_RS13810 V474_RS00550
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 V474_RS15950 V474_RS07795
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) V474_RS11830
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) V474_RS11830
aruH L-arginine:pyruvate transaminase V474_RS13605 V474_RS00235
aruI 2-ketoarginine decarboxylase V474_RS04395
atoB acetyl-CoA C-acetyltransferase V474_RS02980 V474_RS05390
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) V474_RS04345
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) V474_RS15730 V474_RS07795
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 V474_RS08715
davD glutarate semialdehyde dehydrogenase V474_RS17175 V474_RS22325
davT 5-aminovalerate aminotransferase V474_RS13815 V474_RS23835
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase V474_RS01310 V474_RS16345
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase V474_RS17855 V474_RS22775
gabD succinate semialdehyde dehydrogenase V474_RS17175 V474_RS22325
gabT gamma-aminobutyrate transaminase V474_RS13815 V474_RS23835
gbamidase guanidinobutyramidase V474_RS03230
gbuA guanidinobutyrase V474_RS23580
gcdG succinyl-CoA:glutarate CoA-transferase V474_RS01235 V474_RS17140
gcdH glutaryl-CoA dehydrogenase V474_RS05240 V474_RS22780
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase V474_RS12520 V474_RS10060
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) V474_RS13815 V474_RS13220
patD gamma-aminobutyraldehyde dehydrogenase V474_RS10060 V474_RS12520
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase V474_RS20495 V474_RS08705
PRO3 pyrroline-5-carboxylate reductase V474_RS11475
puo putrescine oxidase
put1 proline dehydrogenase V474_RS22455
putA L-glutamate 5-semialdeyde dehydrogenase V474_RS22455 V474_RS22325
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase V474_RS10060 V474_RS12520
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase V474_RS22455 V474_RS22325
rocD ornithine aminotransferase V474_RS13220 V474_RS13815
rocF arginase V474_RS23580
speB agmatinase V474_RS23580

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 Sep 24 2021. 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