Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_164924158.1 NGR_RS12135 aspartate aminotransferase family protein
Query= curated2:Q4A0N2 (394 letters) >NCBI__GCF_000018545.1:WP_164924158.1 Length = 399 Score = 249 bits (636), Expect = 1e-70 Identities = 137/370 (37%), Positives = 209/370 (56%), Gaps = 8/370 (2%) Query: 19 LKLALAKGRGAKVWDIEDNC--YIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRAL 76 L+ L RG VW I ++ Y+D +G +V + GH HP +++AL+ Q++++ VS Sbjct: 12 LRAPLRFERGEGVWLIAEDGTRYLDFAAGVAVNSLGHAHPHLVEALKAQAEKLWHVSNLY 71 Query: 77 YSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMNG 136 ++ + + V N+G EA+E AIK AR++ +I G Sbjct: 72 DVPGQESLARRLTAVTFADRVFFTNSGAEALECAIKTARRY--HFAKGHPERFHVITFEG 129 Query: 137 NFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQGEG 196 FHGRT+ +++ Q Y +GFGP + FGDI +K IN++T AI++EPIQGEG Sbjct: 130 AFHGRTIATIAAGGQQKYIEGFGPKAPGFYQVPFGDIAAVKNAINDETAAILIEPIQGEG 189 Query: 197 GVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLGG 256 G+ + F+QE+R LC+EY +LLI DE+Q G+GRTGK+FA EW PDI + K +GG Sbjct: 190 GIRLASKEFMQELRALCDEYGLLLILDEVQCGVGRTGKLFAHEWSGITPDIMAVAKGIGG 249 Query: 257 GLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDRL 316 G +P+ A LA + + + GTHGST+GGNPLA AV A LDV+ E ++N D+ Sbjct: 250 G-FPLGACLATEAAAAGMVAGTHGSTYGGNPLAMAVGNAVLDVVLAEGFLENVRDVALVF 308 Query: 317 LKHLQQIES---ELIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQGNIIRIAPP 373 + L ++ ++I E+RG GL +GI+ V D + + + +L N++R+ PP Sbjct: 309 RQGLASLKDRFPDVIEEIRGDGLMLGIKAKVPCADVLKAIRAEKLLAVPAGENVLRLLPP 368 Query: 374 LVIDKDEIDE 383 L+ E E Sbjct: 369 LITTAAEARE 378 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: 354 Number of extensions: 13 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 394 Length of database: 399 Length adjustment: 31 Effective length of query: 363 Effective length of database: 368 Effective search space: 133584 Effective search space used: 133584 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 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