GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Sphingobium czechense LL01

Best path

rocE, adiA, aguA, aguB, patA, patD, 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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase V473_RS09530
aguB N-carbamoylputrescine hydrolase V473_RS09535
patA putrescine aminotransferase (PatA/SpuC) V473_RS20290 V473_RS02290
patD gamma-aminobutyraldehyde dehydrogenase V473_RS05540 V473_RS05490
gabT gamma-aminobutyrate transaminase V473_RS20290 V473_RS02290
gabD succinate semialdehyde dehydrogenase V473_RS08475 V473_RS20730
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase
arcB ornithine carbamoyltransferase V473_RS02295 V473_RS11315
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 V473_RS03740 V473_RS04645
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) V473_RS06010
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) V473_RS06010
aruH L-arginine:pyruvate transaminase V473_RS02585 V473_RS14940
aruI 2-ketoarginine decarboxylase V473_RS09680 V473_RS22080
astA arginine N-succinyltransferase V473_RS06010
astB N-succinylarginine dihydrolase V473_RS06005
astC succinylornithine transaminase V473_RS02290 V473_RS20290
astD succinylglutamate semialdehyde dehydrogenase V473_RS10010 V473_RS10045
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase V473_RS07145 V473_RS00635
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) V473_RS04115 V473_RS03035
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) V473_RS04120 V473_RS13485
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 V473_RS03185
davD glutarate semialdehyde dehydrogenase V473_RS08475 V473_RS20300
davT 5-aminovalerate aminotransferase V473_RS02290 V473_RS18720
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase V473_RS04380 V473_RS05770
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase V473_RS00615 V473_RS18225
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase V473_RS03945 V473_RS04050
gcdG succinyl-CoA:glutarate CoA-transferase V473_RS05465 V473_RS08220
gcdH glutaryl-CoA dehydrogenase V473_RS17395 V473_RS17555
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase V473_RS05540 V473_RS05490
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase V473_RS06170
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
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 V473_RS11780
puo putrescine oxidase
put1 proline dehydrogenase V473_RS05455
putA L-glutamate 5-semialdeyde dehydrogenase V473_RS05455 V473_RS05490
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase V473_RS05540 V473_RS05490
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase V473_RS05455 V473_RS05490
rocD ornithine aminotransferase V473_RS02290
rocF arginase V473_RS04050 V473_RS04000
speB agmatinase V473_RS03945 V473_RS04000

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