Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate PP_4481 PP_4481 Succinylornithine transaminase/acetylornithine aminotransferase
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Putida:PP_4481 Length = 406 Score = 255 bits (651), Expect = 2e-72 Identities = 142/381 (37%), Positives = 212/381 (55%), Gaps = 9/381 (2%) Query: 9 DKYSSKNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQR 68 D+ NYSP +G G++VWD ID G +V GHCHP ++KAL EQ+ Sbjct: 14 DQVMVPNYSPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVNALGHCHPALVKALTEQANT 73 Query: 69 ITMVSRALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESS 128 + VS ++ + K+ + N+G E+ E A K+AR+ D Sbjct: 74 LWHVSNVFTNEPALRLAHKLVDATFADRAFFCNSGAESNEAAFKLARRVAHD--RFGPQK 131 Query: 129 SEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAII 188 EIIA +FHGRTL ++S+ Q Y GFGP + I + + D+E LK I+++T A++ Sbjct: 132 HEIIATVNSFHGRTLFTVSVGGQPKYSDGFGPKITGISHVPYNDLEALKAQISDKTCAVV 191 Query: 189 LEPIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIY 248 +EPIQGE GV +++ R+LC+E+N LLI DE+Q G+GRTG ++A + PDI Sbjct: 192 IEPIQGESGVVPADKAYLEGARKLCDEHNALLIFDEVQTGVGRTGSLYAYQHYGVIPDIL 251 Query: 249 LLGKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQN 308 KSLGGG +PI A+L ++ L GTHG+T+GGNPL CAV+ A LDV+N + Sbjct: 252 TSAKSLGGG-FPIGAMLTTTELAKHLAVGTHGTTYGGNPLGCAVACAVLDVVNTPETLAG 310 Query: 309 ALDLGDRLLKHLQQI--ESELIVEVRGRGLFIGIELNVAAQDYCEQMIN----KGVLCKE 362 +R L+QI + L +VRG GL +G L A + + ++N +GV+ + Sbjct: 311 IKAKHERFKTRLEQIGQQYNLFSQVRGVGLLLGCVLTEAWKGKAKDVLNAAEKEGVMVLQ 370 Query: 363 TQGNIIRIAPPLVIDKDEIDE 383 +++R AP LV++ +IDE Sbjct: 371 AGPDVVRFAPSLVVEDADIDE 391 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: 357 Number of extensions: 16 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: 406 Length adjustment: 31 Effective length of query: 363 Effective length of database: 375 Effective search space: 136125 Effective search space used: 136125 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 Sep 17 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