GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Methylocella silvestris BL2

Best path

braC, braD, braE, braF, braG, 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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC MSIL_RS10660
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) MSIL_RS10635
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) MSIL_RS10640
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) MSIL_RS00330 MSIL_RS10645
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) MSIL_RS10650 MSIL_RS00325
rocF arginase
rocD ornithine aminotransferase MSIL_RS08460 MSIL_RS14670
PRO3 pyrroline-5-carboxylate reductase MSIL_RS05865
put1 proline dehydrogenase MSIL_RS08455 MSIL_RS13425
putA L-glutamate 5-semialdeyde dehydrogenase MSIL_RS08455 MSIL_RS19705
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) MSIL_RS01155
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase MSIL_RS04285 MSIL_RS19540
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 MSIL_RS15415 MSIL_RS05500
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) MSIL_RS08680
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA MSIL_RS08670 MSIL_RS05565
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 MSIL_RS15080
aruI 2-ketoarginine decarboxylase MSIL_RS15345
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase MSIL_RS03190
astC succinylornithine transaminase MSIL_RS04290 MSIL_RS08460
astD succinylglutamate semialdehyde dehydrogenase MSIL_RS07550 MSIL_RS08455
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase MSIL_RS15280 MSIL_RS08880
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 MSIL_RS03830
davD glutarate semialdehyde dehydrogenase MSIL_RS17445 MSIL_RS19705
davT 5-aminovalerate aminotransferase MSIL_RS04290 MSIL_RS08460
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase MSIL_RS07135 MSIL_RS04665
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase MSIL_RS07135 MSIL_RS08875
gabD succinate semialdehyde dehydrogenase MSIL_RS08690 MSIL_RS19705
gabT gamma-aminobutyrate transaminase MSIL_RS04290 MSIL_RS08460
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 MSIL_RS19705 MSIL_RS11965
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) MSIL_RS19180
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase MSIL_RS01155 MSIL_RS05960
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) MSIL_RS14670 MSIL_RS08460
patD gamma-aminobutyraldehyde dehydrogenase MSIL_RS19705 MSIL_RS11965
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 MSIL_RS13420 MSIL_RS02165
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase MSIL_RS19705 MSIL_RS11965
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase MSIL_RS08455 MSIL_RS19705
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