Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate 207835 DVU2347 acetylornithine aminotransferase
Query= curated2:Q4A0N2 (394 letters) >MicrobesOnline__882:207835 Length = 399 Score = 247 bits (630), Expect = 5e-70 Identities = 124/384 (32%), Positives = 217/384 (56%), Gaps = 6/384 (1%) Query: 14 KNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVS 73 + Y +++ + G+++WD E YID +SG +V + GHCHP++ + + Q++++ VS Sbjct: 18 RTYGRYPISVQRAEGSRMWDHEGREYIDLLSGIAVTSLGHCHPELAEVMARQARKLVHVS 77 Query: 74 RALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIA 133 Y + EK+ + N+G EA E AIK+AR++ ++ +D + E++ Sbjct: 78 NLFYQEEQLDLAEKLLSTLHCTKAFFCNSGAEANEAAIKLARRYMQRVRGVD--AHEVVT 135 Query: 134 MNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQ 193 + G FHGRTL +++ + Q+ ++ GF P+ A++GDI+ L+ I T +++E +Q Sbjct: 136 LTGAFHGRTLATVAATGQERFQDGFAPMPAGFRQAEWGDIDALRAAITPATAGVLVEMVQ 195 Query: 194 GEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKS 253 GEGGV + + V LC E VLL+ DEIQ GL RTG+ +A + EPDI K+ Sbjct: 196 GEGGVRPMTQDYARAVADLCREKGVLLMVDEIQTGLCRTGRFWAHQHYGVEPDIVTSAKA 255 Query: 254 LGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLG 313 L GL P+ A++ +V G+H +TFG L +V+ A LD++ + L + A +G Sbjct: 256 LANGL-PMGAMMTTDEVAQGFVAGSHATTFGAGALVSSVAAATLDIMKRDRLDERATAVG 314 Query: 314 DRLLKHLQQIESEL---IVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQGNIIRI 370 R ++ + I ++L I EVRG GL IGI L + ++ ++++ +G +C TQ ++R+ Sbjct: 315 GRAMERFRAIGAKLPGTIEEVRGYGLMIGIVLTFSGKEVWKELVARGFVCNNTQEKVLRL 374 Query: 371 APPLVIDKDEIDEVIRVITEVLEK 394 P L ID+ ++ + ++L + Sbjct: 375 VPALTIDEADLTAFADTLEDILAR 398 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: 339 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: 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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