Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate 8502443 DvMF_3149 acetylornithine aminotransferase (RefSeq)
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Miya:8502443 Length = 402 Score = 223 bits (568), Expect = 8e-63 Identities = 117/382 (30%), Positives = 208/382 (54%), Gaps = 6/382 (1%) Query: 14 KNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVS 73 + Y +++A+G+G+++WD++ Y+D +SG +V + GHCH ++ + Q++++ VS Sbjct: 18 RTYGRYPISVARGQGSRLWDVDGREYVDLLSGIAVTSLGHCHEELAEVAAAQARKLVHVS 77 Query: 74 RALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIA 133 Y + E++ ++ N+G EA E AIK+AR++ ++ + EII Sbjct: 78 NLFYQEEQLDLAERLLSTSHCTKAFFCNSGAEANEAAIKLARRYMQRVQG--REAYEIIT 135 Query: 134 MNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQ 193 + G FHGRTL +++ + Q ++ GF P+ GDIE L+ I QT +++E +Q Sbjct: 136 LTGAFHGRTLATVAATGQAKFQDGFYPMPEGFRQVPSGDIEALRAAIGPQTAGVLVEVVQ 195 Query: 194 GEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKS 253 GEGGV + + V+ LC E VL + DEIQ G+ RTG+ ++ + EPDI K+ Sbjct: 196 GEGGVCPLDPDYARAVQALCREKGVLFMTDEIQAGMCRTGRFWSFQNYGLEPDIVSCAKA 255 Query: 254 LGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLG 313 L GL P+ A++ +V G+H +TFG L AV+ ++++ + L A G Sbjct: 256 LANGL-PMGAMMTTDEVARGFVAGSHATTFGAGALVSAVASRTVEIMLRDDLAGRAATEG 314 Query: 314 DRLLKHLQQIESEL---IVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQGNIIRI 370 R++ + + +L I VRG GL IG+ L ++ + +I++G +C TQ ++R+ Sbjct: 315 ARIMDRFRAMGQKLPGTIDHVRGLGLMIGVVLAFPGKEVWQALIDRGFICNLTQDCVLRL 374 Query: 371 APPLVIDKDEIDEVIRVITEVL 392 P L I + ++D + ++L Sbjct: 375 LPALTIPRADLDAFADALEDIL 396 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: 314 Number of extensions: 11 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: 402 Length adjustment: 31 Effective length of query: 363 Effective length of database: 371 Effective search space: 134673 Effective search space used: 134673 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