GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Methylobacterium nodulans ORS 2060

Best path

braC, braD, braE, braF, braG, 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 (44 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 MNOD_RS08385 MNOD_RS14755
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) MNOD_RS08415 MNOD_RS31080
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) MNOD_RS08410 MNOD_RS05615
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) MNOD_RS08405 MNOD_RS01650
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) MNOD_RS08395 MNOD_RS05610
rocF arginase MNOD_RS05870 MNOD_RS36320
ocd ornithine cyclodeaminase MNOD_RS05875 MNOD_RS14815
put1 proline dehydrogenase MNOD_RS06935 MNOD_RS37755
putA L-glutamate 5-semialdeyde dehydrogenase MNOD_RS06935 MNOD_RS36935
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) MNOD_RS01410
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase MNOD_RS35295 MNOD_RS15635
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 MNOD_RS24395 MNOD_RS31675
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) MNOD_RS24385 MNOD_RS04315
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA MNOD_RS24380 MNOD_RS21100
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) MNOD_RS24390 MNOD_RS11495
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase MNOD_RS09470 MNOD_RS08070
aruI 2-ketoarginine decarboxylase MNOD_RS36560 MNOD_RS37675
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase MNOD_RS35300 MNOD_RS21735
astD succinylglutamate semialdehyde dehydrogenase MNOD_RS36555 MNOD_RS12075
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase MNOD_RS27980 MNOD_RS18795
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase MNOD_RS22070 MNOD_RS36555
davT 5-aminovalerate aminotransferase MNOD_RS35300 MNOD_RS21735
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase MNOD_RS00720 MNOD_RS18785
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase MNOD_RS15890 MNOD_RS24770
gabD succinate semialdehyde dehydrogenase MNOD_RS22070 MNOD_RS36555
gabT gamma-aminobutyrate transaminase MNOD_RS26085 MNOD_RS13870
gbamidase guanidinobutyramidase MNOD_RS28150
gbuA guanidinobutyrase MNOD_RS36320
gcdG succinyl-CoA:glutarate CoA-transferase MNOD_RS06105 MNOD_RS13190
gcdH glutaryl-CoA dehydrogenase MNOD_RS06130 MNOD_RS01425
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase MNOD_RS07620 MNOD_RS35765
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) MNOD_RS25695
odc L-ornithine decarboxylase MNOD_RS01410 MNOD_RS07925
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) MNOD_RS13870 MNOD_RS26085
patD gamma-aminobutyraldehyde dehydrogenase MNOD_RS36935 MNOD_RS32090
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase MNOD_RS18775 MNOD_RS18730
PRO3 pyrroline-5-carboxylate reductase MNOD_RS06575 MNOD_RS38995
puo putrescine oxidase
puuA glutamate-putrescine ligase MNOD_RS16000
puuB gamma-glutamylputrescine oxidase MNOD_RS17215 MNOD_RS11485
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase MNOD_RS07620 MNOD_RS35765
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase MNOD_RS06935 MNOD_RS36935
rocD ornithine aminotransferase MNOD_RS26085 MNOD_RS21735
rocE L-arginine permease MNOD_RS23565 MNOD_RS04385
speB agmatinase MNOD_RS36320

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