GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Algoriphagus machipongonensis PR1

Best path

rocE, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
rocF arginase ALPR1_RS12720
rocD ornithine aminotransferase ALPR1_RS04740 ALPR1_RS09710
PRO3 pyrroline-5-carboxylate reductase ALPR1_RS12575
put1 proline dehydrogenase ALPR1_RS14990
putA L-glutamate 5-semialdeyde dehydrogenase ALPR1_RS17935 ALPR1_RS01205
Alternative steps:
AAP3 L-arginine transporter AAP3
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase ALPR1_RS07470
aguB N-carbamoylputrescine hydrolase ALPR1_RS07465
arcA arginine deiminase ALPR1_RS14970
arcB ornithine carbamoyltransferase ALPR1_RS11240
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 ALPR1_RS04965 ALPR1_RS06390
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 ALPR1_RS18160 ALPR1_RS15015
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase ALPR1_RS03490 ALPR1_RS04740
astD succinylglutamate semialdehyde dehydrogenase ALPR1_RS01205 ALPR1_RS06860
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase ALPR1_RS13240 ALPR1_RS01085
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) ALPR1_RS03040
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) ALPR1_RS03040 ALPR1_RS06695
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase ALPR1_RS01205 ALPR1_RS06445
davT 5-aminovalerate aminotransferase ALPR1_RS03490 ALPR1_RS09710
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase ALPR1_RS16285 ALPR1_RS07745
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase ALPR1_RS01095 ALPR1_RS10470
gabD succinate semialdehyde dehydrogenase ALPR1_RS06445 ALPR1_RS01205
gabT gamma-aminobutyrate transaminase ALPR1_RS03490 ALPR1_RS09710
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase ALPR1_RS12195 ALPR1_RS19490
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase ALPR1_RS06860 ALPR1_RS01205
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) ALPR1_RS11810
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 ALPR1_RS05125
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
patA putrescine aminotransferase (PatA/SpuC) ALPR1_RS09710 ALPR1_RS03490
patD gamma-aminobutyraldehyde dehydrogenase ALPR1_RS01205 ALPR1_RS06860
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase ALPR1_RS03510
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase ALPR1_RS06860 ALPR1_RS01205
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase ALPR1_RS17935 ALPR1_RS01205
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