Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate BPHYT_RS15580 BPHYT_RS15580 acetylornithine aminotransferase
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__BFirm:BPHYT_RS15580 Length = 394 Score = 225 bits (574), Expect = 1e-63 Identities = 131/379 (34%), Positives = 213/379 (56%), Gaps = 10/379 (2%) Query: 20 KLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRALYSD 79 ++ G+G+ ++D Y+D I G++V + GHC+ +I+AL +QSQ + S A Y+ Sbjct: 19 EIVFTHGKGSWLYDNNGKRYLDFIQGWAVNSLGHCNDGMIEALNKQSQLLINPSPAFYNQ 78 Query: 80 NLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMNGNFH 139 + + + + + + V N+G EA E AIK+ARKWG K + + EII + +FH Sbjct: 79 PMAQLAGLLTQHSCFDKVFFANSGAEANEGAIKLARKWG---KKFKDGAFEIITFDHSFH 135 Query: 140 GRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQGEGGVN 199 GRTL ++S S + + + P + AD DI ++KLIN +T A++LEPIQGEGGV Sbjct: 136 GRTLATMSASGKPGWDTIYAPQVPGFPKADLNDIASVEKLINAKTVAVMLEPIQGEGGVI 195 Query: 200 IPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLGGGLY 259 F+Q++R+L ++N+LLI DE+Q G GR G +FA E + EPDI LGK +GGG+ Sbjct: 196 PATREFMQQLRELTKKHNLLLIVDEVQSGCGRAGTLFAYELSDIEPDIMTLGKGIGGGV- 254 Query: 260 PISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDRLLKH 319 P++A+LA ++ +V G G T+ GNPL AV + + L ++ G+ L Sbjct: 255 PLAALLAKAEI-AVFEAGDQGGTYNGNPLMTAVGYSVISQLTAPGFLEGLRARGEYLRAK 313 Query: 320 LQQIESELIVE-VRGRG----LFIGIELNVAAQDYCEQMINKGVLCKETQGNIIRIAPPL 374 L ++ E E RG G L +G ++ + M G+L + N++R P L Sbjct: 314 LLELSEERGFEGERGEGLLRALLLGKDIGNQIVEKARDMQPDGLLLNAARPNLLRFMPAL 373 Query: 375 VIDKDEIDEVIRVITEVLE 393 + +EID+++ ++ +L+ Sbjct: 374 NVTNEEIDQMMTMLRSILD 392 Lambda K H 0.317 0.136 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 326 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 394 Length of database: 394 Length adjustment: 31 Effective length of query: 363 Effective length of database: 363 Effective search space: 131769 Effective search space used: 131769 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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