GapMind for catabolism of small carbon sources


L-arginine catabolism in Klebsiella michiganensis M5al

Best path

artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD

Also see fitness data for the top candidates


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
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT BWI76_RS20335 BWI76_RS20340
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) BWI76_RS20325 BWI76_RS09505
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA BWI76_RS20320 BWI76_RS09520
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) BWI76_RS09510 BWI76_RS20330
adiA arginine decarboxylase (AdiA/SpeA) BWI76_RS24030 BWI76_RS05300
speB agmatinase BWI76_RS24025 BWI76_RS21880
puuA glutamate-putrescine ligase BWI76_RS10710 BWI76_RS00400
puuB gamma-glutamylputrescine oxidase BWI76_RS10690
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BWI76_RS10695 BWI76_RS03865
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase BWI76_RS10705
gabT gamma-aminobutyrate transaminase BWI76_RS26375 BWI76_RS14455
gabD succinate semialdehyde dehydrogenase BWI76_RS05620 BWI76_RS10695
Alternative steps:
AAP3 L-arginine transporter AAP3
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase BWI76_RS03010 BWI76_RS17500
arcC carbamate kinase BWI76_RS07060 BWI76_RS17520
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) BWI76_RS11675
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) BWI76_RS11675
aruH L-arginine:pyruvate transaminase BWI76_RS10245 BWI76_RS07920
aruI 2-ketoarginine decarboxylase BWI76_RS27815 BWI76_RS04695
astA arginine N-succinyltransferase BWI76_RS11675
astB N-succinylarginine dihydrolase BWI76_RS11685
astC succinylornithine transaminase BWI76_RS11670 BWI76_RS26000
astD succinylglutamate semialdehyde dehydrogenase BWI76_RS11680 BWI76_RS13425
astE succinylglutamate desuccinylase BWI76_RS11690
atoB acetyl-CoA C-acetyltransferase BWI76_RS23445 BWI76_RS01360
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 BWI76_RS26350 BWI76_RS26365
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BWI76_RS26345 BWI76_RS07280
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BWI76_RS26340 BWI76_RS07275
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BWI76_RS26335 BWI76_RS07270
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BWI76_RS26330 BWI76_RS05975
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase BWI76_RS05620 BWI76_RS03865
davT 5-aminovalerate aminotransferase BWI76_RS26375 BWI76_RS14020
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BWI76_RS13115 BWI76_RS20455
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BWI76_RS01365 BWI76_RS20455
gbamidase guanidinobutyramidase
gbuA guanidinobutyrase BWI76_RS21880 BWI76_RS21925
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase BWI76_RS10695 BWI76_RS03865
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase BWI76_RS24175 BWI76_RS07195
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) BWI76_RS24630 BWI76_RS14455
patD gamma-aminobutyraldehyde dehydrogenase BWI76_RS13425 BWI76_RS10695
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 BWI76_RS06170 BWI76_RS14970
puo putrescine oxidase BWI76_RS13080
put1 proline dehydrogenase BWI76_RS10795
putA L-glutamate 5-semialdeyde dehydrogenase BWI76_RS10795 BWI76_RS07615
rocA 1-pyrroline-5-carboxylate dehydrogenase BWI76_RS10795 BWI76_RS07615
rocD ornithine aminotransferase BWI76_RS26375 BWI76_RS14020
rocE L-arginine permease BWI76_RS06025 BWI76_RS19685
rocF arginase BWI76_RS21880 BWI76_RS21925

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 17 2021. The underlying query database was built on Sep 17 2021.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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