GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Mesorhizobium ciceri biovar biserrulae WSM1271

Best path

braC, braD, braE, braF, braG, aruH, aruI, kauB, gbuA, gabT, gabD

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 (46 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 MESCI_RS06170 MESCI_RS24305
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) MESCI_RS06145 MESCI_RS31055
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) MESCI_RS06150 MESCI_RS31060
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) MESCI_RS06155 MESCI_RS31065
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) MESCI_RS06160 MESCI_RS02790
aruH L-arginine:pyruvate transaminase MESCI_RS16770 MESCI_RS09570
aruI 2-ketoarginine decarboxylase MESCI_RS01575 MESCI_RS26295
kauB 4-guanidinobutyraldehyde dehydrogenase MESCI_RS13255 MESCI_RS03435
gbuA guanidinobutyrase MESCI_RS02840 MESCI_RS22265
gabT gamma-aminobutyrate transaminase MESCI_RS00215 MESCI_RS17105
gabD succinate semialdehyde dehydrogenase MESCI_RS28355 MESCI_RS26965
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA) MESCI_RS09615
aguA agmatine deiminase MESCI_RS23895
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase MESCI_RS29880 MESCI_RS20165
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 MESCI_RS29850 MESCI_RS19705
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) MESCI_RS13050 MESCI_RS19715
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA MESCI_RS33060 MESCI_RS01590
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) MESCI_RS01600 MESCI_RS13055
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase MESCI_RS29885 MESCI_RS00215
astD succinylglutamate semialdehyde dehydrogenase MESCI_RS28355 MESCI_RS24670
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase MESCI_RS06630 MESCI_RS05450
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 MESCI_RS17265 MESCI_RS28355
davT 5-aminovalerate aminotransferase MESCI_RS00215 MESCI_RS29885
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase MESCI_RS30135 MESCI_RS23380
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase MESCI_RS05330 MESCI_RS29955
gbamidase guanidinobutyramidase MESCI_RS07990
gcdG succinyl-CoA:glutarate CoA-transferase MESCI_RS15670 MESCI_RS01310
gcdH glutaryl-CoA dehydrogenase MESCI_RS09970 MESCI_RS24275
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) MESCI_RS12230
ocd ornithine cyclodeaminase MESCI_RS28145 MESCI_RS12565
odc L-ornithine decarboxylase MESCI_RS09615
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 MESCI_RS29690
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) MESCI_RS17105 MESCI_RS28410
patD gamma-aminobutyraldehyde dehydrogenase MESCI_RS00735 MESCI_RS24670
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase MESCI_RS06140 MESCI_RS00880
PRO3 pyrroline-5-carboxylate reductase MESCI_RS12035
puo putrescine oxidase
put1 proline dehydrogenase MESCI_RS17295 MESCI_RS00790
putA L-glutamate 5-semialdeyde dehydrogenase MESCI_RS17295 MESCI_RS01365
puuA glutamate-putrescine ligase MESCI_RS12150 MESCI_RS05425
puuB gamma-glutamylputrescine oxidase MESCI_RS05430 MESCI_RS12140
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase MESCI_RS13255 MESCI_RS03435
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase MESCI_RS01730
rocA 1-pyrroline-5-carboxylate dehydrogenase MESCI_RS17295 MESCI_RS01365
rocD ornithine aminotransferase MESCI_RS00215 MESCI_RS26490
rocE L-arginine permease
rocF arginase MESCI_RS28140 MESCI_RS02840
speB agmatinase MESCI_RS22265 MESCI_RS02840

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