Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate 5208066 Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__PV4:5208066 Length = 405 Score = 254 bits (648), Expect = 4e-72 Identities = 142/381 (37%), Positives = 218/381 (57%), Gaps = 9/381 (2%) Query: 9 DKYSSKNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQR 68 D+ NY+P + +G G++VWD E N ++D G +V GHCHP ++ AL+EQ ++ Sbjct: 13 DEVMVPNYAPSAVIPVRGEGSRVWDQEGNEFVDFAGGIAVNCLGHCHPALVGALKEQGEK 72 Query: 69 ITMVSRALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESS 128 I ++ + ++ K+ + E V N+G EA E A+K+AR++ D Sbjct: 73 IWHLANVMTNEPALALATKLVEATFAEKVYFANSGAEANEAALKLARRYALD--KFGAEK 130 Query: 129 SEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAII 188 +IIA + FHGRT ++S+ Q +Y GFGP +I + F DI L+ ++++T AI+ Sbjct: 131 DQIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPFNDIAALEAEVSDKTCAIM 190 Query: 189 LEPIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIY 248 LEP+QGEGG+ F++ VR L +++N L+I DE+Q G+GR G+++A PDI Sbjct: 191 LEPLQGEGGIIDADPEFLRAVRALADKHNALVIFDEVQTGVGRLGELYAYMRTEVTPDIL 250 Query: 249 LLGKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQN 308 K+LGGG +PI+A+L ++ S L GTHGST+GGNPLACA+ A LDV+N ++ Sbjct: 251 TTAKALGGG-FPIAAMLTTTEIASHLKIGTHGSTYGGNPLACAIGNAVLDVVNTPEVLDG 309 Query: 309 ALDLGDRLLKHLQQIESE--LIVEVRGRGLFIGIELNVAAQ----DYCEQMINKGVLCKE 362 L L QI + + EVRG+GL +G LN Q D+ ++G++C Sbjct: 310 VKRREQLLRDGLNQINEKYHVFTEVRGQGLLLGAVLNEQYQGRSKDFLVAGTSEGLMCLI 369 Query: 363 TQGNIIRIAPPLVIDKDEIDE 383 N+IR P LVI + +I E Sbjct: 370 AGPNVIRFTPSLVIPEADIAE 390 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: 366 Number of extensions: 12 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: 405 Length adjustment: 31 Effective length of query: 363 Effective length of database: 374 Effective search space: 135762 Effective search space used: 135762 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