GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Sphingomonas histidinilytica UM2

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 B5X82_RS24315
adiA arginine decarboxylase (AdiA/SpeA)
aguA agmatine deiminase B5X82_RS08125
aguB N-carbamoylputrescine hydrolase B5X82_RS08130
patA putrescine aminotransferase (PatA/SpuC) B5X82_RS16580 B5X82_RS09405
patD gamma-aminobutyraldehyde dehydrogenase B5X82_RS22235 B5X82_RS22960
gabT gamma-aminobutyrate transaminase B5X82_RS11660 B5X82_RS09405
gabD succinate semialdehyde dehydrogenase B5X82_RS11705 B5X82_RS22235
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase
arcB ornithine carbamoyltransferase B5X82_RS09400 B5X82_RS17945
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) B5X82_RS14910
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA B5X82_RS14905 B5X82_RS01540
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) B5X82_RS17595 B5X82_RS17585
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) B5X82_RS17585 B5X82_RS17595
aruH L-arginine:pyruvate transaminase B5X82_RS04015 B5X82_RS00525
aruI 2-ketoarginine decarboxylase B5X82_RS22100 B5X82_RS16650
astA arginine N-succinyltransferase B5X82_RS17595 B5X82_RS17585
astB N-succinylarginine dihydrolase B5X82_RS17590
astC succinylornithine transaminase B5X82_RS09405 B5X82_RS16580
astD succinylglutamate semialdehyde dehydrogenase B5X82_RS17600 B5X82_RS11940
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase B5X82_RS18105 B5X82_RS24295
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)
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) B5X82_RS15520 B5X82_RS22845
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 B5X82_RS10835
davD glutarate semialdehyde dehydrogenase B5X82_RS11705 B5X82_RS22235
davT 5-aminovalerate aminotransferase B5X82_RS11660 B5X82_RS09405
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase B5X82_RS19780 B5X82_RS16280
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase B5X82_RS15560 B5X82_RS24290
gbamidase guanidinobutyramidase B5X82_RS17730
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase B5X82_RS20105 B5X82_RS09500
gcdH glutaryl-CoA dehydrogenase B5X82_RS04280 B5X82_RS20685
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase B5X82_RS22235 B5X82_RS21075
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) B5X82_RS10020
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase B5X82_RS00230
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 B5X82_RS10695
puo putrescine oxidase
put1 proline dehydrogenase B5X82_RS07685
putA L-glutamate 5-semialdeyde dehydrogenase B5X82_RS07685 B5X82_RS15880
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase B5X82_RS22235 B5X82_RS22960
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase B5X82_RS07685 B5X82_RS15880
rocD ornithine aminotransferase B5X82_RS11660 B5X82_RS16580
rocF arginase
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