Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate CCNA_00620 CCNA_00620 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Caulo:CCNA_00620 Length = 392 Score = 240 bits (613), Expect = 4e-68 Identities = 136/372 (36%), Positives = 208/372 (55%), Gaps = 8/372 (2%) Query: 16 YSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRA 75 Y+ + + +G G ++D + Y+D +G +V GH P++++AL+ Q+ + S Sbjct: 8 YARANIDIVRGEGCWLYDQDGRDYLDLAAGVAVNTLGHGDPRLVQALKTQADILWHASNL 67 Query: 76 LYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKW-GADIKNIDESSSEIIAM 134 K+ + V N+G EAVE AIK AR+W GA + ++ Sbjct: 68 YRLPAQEALATKLTDATFADRVFFANSGAEAVEAAIKTARRWQGAKGR---PERYRVLTF 124 Query: 135 NGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQG 194 FHGRTL ++S + Q ++GF PL + F DIE + I QT AI++EPIQG Sbjct: 125 GNAFHGRTLATISATDQMKVREGFTPLYDAFDTTPFNDIEGAARAITPQTAAILVEPIQG 184 Query: 195 EGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSL 254 EGG+ F+ +R LC+++++LLI DE+Q G+GRTG +FA E PDI + K L Sbjct: 185 EGGLTPATPGFLAGLRALCDQHDLLLILDEVQTGIGRTGHLFAHELYGVRPDIIAVAKGL 244 Query: 255 GGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALD--- 311 GGG +PI A LA +D S +TPG+HGST+GGNPLACAV+ A LD + ++ + Sbjct: 245 GGG-FPIGACLATEDAASGMTPGSHGSTYGGNPLACAVASAVLDAVLAPGFLETVRERAA 303 Query: 312 LGDRLLKHLQQIESELIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQGNIIRIA 371 L D LL+ L + S+L V +G GL G+++ +A+D + + GV+ +++R+ Sbjct: 304 LVDALLERLLRRHSDLFVRAQGHGLMRGLQVRASARDVVAHLRDFGVMTVAAGADVVRLL 363 Query: 372 PPLVIDKDEIDE 383 PPL I + EI E Sbjct: 364 PPLTISELEIAE 375 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: 338 Number of extensions: 17 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: 392 Length adjustment: 31 Effective length of query: 363 Effective length of database: 361 Effective search space: 131043 Effective search space used: 131043 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