braC, braD, braE, braF, braG, rocF, ocd, put1, putA
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.
Or see definitions of steps
Step | Description | Best candidate | 2nd candidate |
---|---|---|---|
braC | ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC | BIBO1_RS12225 | BIBO1_RS12220 |
braD | ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | BIBO1_RS12250 | BIBO1_RS14975 |
braE | ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | BIBO1_RS12245 | |
braF | ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | BIBO1_RS12240 | BIBO1_RS19765 |
braG | ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) | BIBO1_RS12235 | BIBO1_RS14990 |
rocF | arginase | BIBO1_RS18720 | BIBO1_RS07375 |
ocd | ornithine cyclodeaminase | BIBO1_RS18715 | |
put1 | proline dehydrogenase | BIBO1_RS16940 | BIBO1_RS12740 |
putA | L-glutamate 5-semialdeyde dehydrogenase | BIBO1_RS16940 | BIBO1_RS10860 |
Alternative steps: | |||
AAP3 | L-arginine transporter AAP3 | ||
adiA | arginine decarboxylase (AdiA/SpeA) | ||
aguA | agmatine deiminase | ||
aguB | N-carbamoylputrescine hydrolase | ||
arcA | arginine deiminase | ||
arcB | ornithine carbamoyltransferase | BIBO1_RS13060 | BIBO1_RS17780 |
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 | BIBO1_RS07950 | BIBO1_RS09035 |
artM | L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) | BIBO1_RS07940 | BIBO1_RS17105 |
artP | L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA | BIBO1_RS07180 | BIBO1_RS20000 |
artQ | L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) | BIBO1_RS07945 | BIBO1_RS14880 |
aruF | ornithine/arginine N-succinyltransferase subunit AruAI (AruF) | ||
aruG | ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | ||
aruH | L-arginine:pyruvate transaminase | BIBO1_RS11000 | |
aruI | 2-ketoarginine decarboxylase | BIBO1_RS18945 | |
astA | arginine N-succinyltransferase | ||
astB | N-succinylarginine dihydrolase | ||
astC | succinylornithine transaminase | BIBO1_RS13055 | BIBO1_RS18510 |
astD | succinylglutamate semialdehyde dehydrogenase | BIBO1_RS17145 | BIBO1_RS10860 |
astE | succinylglutamate desuccinylase | ||
atoB | acetyl-CoA C-acetyltransferase | BIBO1_RS17190 | BIBO1_RS16830 |
bgtB | L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | ||
Can1 | L-arginine transporter Can1 | ||
CAT1 | L-arginine transporter CAT1 | ||
davD | glutarate semialdehyde dehydrogenase | BIBO1_RS11605 | BIBO1_RS17145 |
davT | 5-aminovalerate aminotransferase | BIBO1_RS13055 | BIBO1_RS18510 |
ech | (S)-3-hydroxybutanoyl-CoA hydro-lyase | BIBO1_RS06755 | BIBO1_RS15870 |
fadB | (S)-3-hydroxybutanoyl-CoA dehydrogenase | BIBO1_RS18180 | BIBO1_RS05845 |
gabD | succinate semialdehyde dehydrogenase | BIBO1_RS11605 | BIBO1_RS15485 |
gabT | gamma-aminobutyrate transaminase | BIBO1_RS10785 | BIBO1_RS15460 |
gbamidase | guanidinobutyramidase | BIBO1_RS12585 | |
gbuA | guanidinobutyrase | BIBO1_RS07375 | |
gcdG | succinyl-CoA:glutarate CoA-transferase | BIBO1_RS15880 | BIBO1_RS08425 |
gcdH | glutaryl-CoA dehydrogenase | BIBO1_RS08430 | BIBO1_RS17185 |
glaH | glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) | ||
kauB | 4-guanidinobutyraldehyde dehydrogenase | BIBO1_RS15485 | BIBO1_RS10835 |
lhgD | L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) | BIBO1_RS19215 | |
odc | L-ornithine decarboxylase | BIBO1_RS15590 | |
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) | BIBO1_RS10785 | BIBO1_RS15460 |
patD | gamma-aminobutyraldehyde dehydrogenase | BIBO1_RS20005 | BIBO1_RS14100 |
prdA | D-proline reductase, prdA component | ||
prdB | D-proline reductase, prdB component | ||
prdC | D-proline reductase, electron transfer component PrdC | ||
prdF | proline racemase | BIBO1_RS12255 | BIBO1_RS13215 |
PRO3 | pyrroline-5-carboxylate reductase | BIBO1_RS18120 | BIBO1_RS18355 |
puo | putrescine oxidase | ||
puuA | glutamate-putrescine ligase | BIBO1_RS18050 | BIBO1_RS16895 |
puuB | gamma-glutamylputrescine oxidase | BIBO1_RS18060 | BIBO1_RS19990 |
puuC | gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | BIBO1_RS15485 | BIBO1_RS10835 |
puuD | gamma-glutamyl-gamma-aminobutyrate hydrolase | BIBO1_RS19105 | |
rocA | 1-pyrroline-5-carboxylate dehydrogenase | BIBO1_RS16940 | BIBO1_RS10860 |
rocD | ornithine aminotransferase | BIBO1_RS13055 | BIBO1_RS10785 |
rocE | L-arginine permease | BIBO1_RS14845 | |
speB | agmatinase | BIBO1_RS07375 |
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.
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:
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