Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_086508150.1 BZY95_RS01045 aspartate aminotransferase family protein
Query= curated2:Q4A0N2 (394 letters) >NCBI__GCF_002151265.1:WP_086508150.1 Length = 404 Score = 260 bits (665), Expect = 4e-74 Identities = 141/392 (35%), Positives = 226/392 (57%), Gaps = 9/392 (2%) Query: 9 DKYSSKNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQR 68 D+Y NYSP K+ +G G+++WD E YID G +V + GHCHP ++KAL EQ + Sbjct: 11 DQYMVPNYSPQKVIPVRGEGSRLWDQEGREYIDFAGGIAVNSLGHCHPVLVKALTEQGNK 70 Query: 69 ITMVSRALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESS 128 + +S ++ K + + + + ++G EA E A+K+AR+W D N E Sbjct: 71 LWHLSNVYTNEPSLKLAKTLVERTFADKAYFCSSGGEANEAALKLARRWAHD--NFGEHK 128 Query: 129 SEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAII 188 I++ +FHGRT ++S+ Q Y +GFGP+ I + +F +++ ++ LIN+ T A++ Sbjct: 129 HRIVSFYQSFHGRTFFTVSVGGQPKYSQGFGPVPGGIVHGEFNNLDSVRDLINDDTCAVM 188 Query: 189 LEPIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIY 248 +EP+QGEGG+ F+Q +R LC+ ++ LLI DE+Q G+GRTG ++A EPDI Sbjct: 189 VEPMQGEGGITPATQEFLQGLRDLCDAHDALLIFDEVQTGVGRTGSLYAYMEYGIEPDIL 248 Query: 249 LLGKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQN 308 K+LGGG +PI A+L V L GTHGST+GGN LA AV++AA++ ++ ++ Sbjct: 249 TSAKALGGG-FPIGAMLTTDRVAPALAIGTHGSTYGGNALASAVALAAVEHIDTPEVLGG 307 Query: 309 ALDLGDRLLKHLQQIESE--LIVEVRGRGLFIGIELNV----AAQDYCEQMINKGVLCKE 362 D +HL+ I + + E+RG GL IG E+ A+D I +G++ Sbjct: 308 VKQRHDLFREHLEAINRKHGVFREIRGMGLLIGAEMTPEYKDRAKDILPLAIEEGLMALI 367 Query: 363 TQGNIIRIAPPLVIDKDEIDEVIRVITEVLEK 394 N++R+AP LVI + +I E + + +E+ Sbjct: 368 AGPNVLRMAPSLVIPEADIAEGMARLERAIER 399 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: 382 Number of extensions: 17 Number of successful extensions: 5 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: 404 Length adjustment: 31 Effective length of query: 363 Effective length of database: 373 Effective search space: 135399 Effective search space used: 135399 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 10 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