GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Streptococcus massiliensis 4401825

Best path

bgtB, artP, arcA, arcB, arcC, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) BN415_RS05885 BN415_RS09690
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA BN415_RS05890 BN415_RS02815
arcA arginine deiminase BN415_RS04515
arcB ornithine carbamoyltransferase BN415_RS04510
arcC carbamate kinase BN415_RS04495
rocD ornithine aminotransferase
rocA 1-pyrroline-5-carboxylate dehydrogenase
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT BN415_RS05885
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) BN415_RS05885 BN415_RS09690
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) BN415_RS09690 BN415_RS05885
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase BN415_RS06885
aruI 2-ketoarginine decarboxylase BN415_RS05920
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase
astD succinylglutamate semialdehyde dehydrogenase
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase
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) BN415_RS07285
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) BN415_RS07275 BN415_RS07270
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BN415_RS07270 BN415_RS07505
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase
davT 5-aminovalerate aminotransferase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BN415_RS08100
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BN415_RS08070
gabD succinate semialdehyde dehydrogenase BN415_RS08155 BN415_RS07850
gabT gamma-aminobutyrate transaminase
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase
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)
patD gamma-aminobutyraldehyde dehydrogenase
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 BN415_RS03050
puo putrescine oxidase
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase
puuA glutamate-putrescine ligase BN415_RS09455
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase BN415_RS01545
rocE L-arginine permease BN415_RS05555
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 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