GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Haloterrigena daqingensis JX313

Best path

rocE, adiA, speB, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
adiA arginine decarboxylase (AdiA/SpeA) BB347_RS16365
speB agmatinase BB347_RS01540 BB347_RS07370
patA putrescine aminotransferase (PatA/SpuC) BB347_RS07365 BB347_RS14645
patD gamma-aminobutyraldehyde dehydrogenase BB347_RS14690 BB347_RS05680
gabT gamma-aminobutyrate transaminase BB347_RS07365 BB347_RS14645
gabD succinate semialdehyde dehydrogenase BB347_RS14690 BB347_RS05680
Alternative steps:
AAP3 L-arginine transporter AAP3
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase BB347_RS12525 BB347_RS04310
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 BB347_RS13945 BB347_RS07330
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 BB347_RS03855 BB347_RS02980
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase BB347_RS12535 BB347_RS07365
astD succinylglutamate semialdehyde dehydrogenase BB347_RS02620 BB347_RS05680
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase BB347_RS04515 BB347_RS02010
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) BB347_RS02480 BB347_RS14205
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BB347_RS02485 BB347_RS06910
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase BB347_RS14690 BB347_RS05680
davT 5-aminovalerate aminotransferase BB347_RS07365 BB347_RS08970
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BB347_RS09135 BB347_RS14695
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BB347_RS01645 BB347_RS09135
gbamidase guanidinobutyramidase BB347_RS04555
gbuA guanidinobutyrase BB347_RS07370 BB347_RS01540
gcdG succinyl-CoA:glutarate CoA-transferase BB347_RS13070 BB347_RS14755
gcdH glutaryl-CoA dehydrogenase BB347_RS11355 BB347_RS14400
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase BB347_RS14690 BB347_RS05680
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase BB347_RS03865
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
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
puo putrescine oxidase BB347_RS01220
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase BB347_RS14690 BB347_RS02620
puuA glutamate-putrescine ligase BB347_RS10035 BB347_RS16575
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BB347_RS14690 BB347_RS03295
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase BB347_RS14690 BB347_RS02620
rocD ornithine aminotransferase BB347_RS08970 BB347_RS07365
rocF arginase BB347_RS06745 BB347_RS01540

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