Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate Ga0059261_4131 Ga0059261_4131 Ornithine/acetylornithine aminotransferase
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Korea:Ga0059261_4131 Length = 398 Score = 221 bits (562), Expect = 4e-62 Identities = 124/376 (32%), Positives = 206/376 (54%), Gaps = 9/376 (2%) Query: 16 YSPLKLALAKGRGAKVWDIEDN-CYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSR 74 Y+ +A +G GA ++ ++ Y+DC++G + GHCHP ++ AL+ Q+ ++ +S Sbjct: 9 YARAPIAFDRGEGAWLYPVDGGEPYLDCVAGVATNALGHCHPVLVAALEAQAAKLWHISN 68 Query: 75 ALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAM 134 E++ + + V N+GTEAVE AIK+AR++ A + +I Sbjct: 69 MFEMPGQNALAERLTTASFADTVFFTNSGTEAVECAIKVARRYHA--ARGEPQRQTVIGF 126 Query: 135 NGNFHGRTLGSLSLSSQDSYKKGFGPLLNN-IHYADFGDIEQLKKLINNQTTAIILEPIQ 193 +G FHGRT G+++ + ++ GFG L +H+A + ++ T A+++EP+Q Sbjct: 127 SGAFHGRTYGAMNAAGNPAHLDGFGDRLPGFVHFAVDNWPALALAIADSATAAVVVEPVQ 186 Query: 194 GEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEW-ENTEPDIYLLGK 252 GEGG F+ ++R C + VLLI DE+Q G+GRTGK+FA +W + PDI L K Sbjct: 187 GEGGARAMTEPFLDKLRAACTAHGVLLIYDEVQTGMGRTGKLFAHQWYPDATPDIMALAK 246 Query: 253 SLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDL 312 +LG G +P+ A LA + S + PG HG+T GGNPLA AV++AA D + + + +A ++ Sbjct: 247 ALGSG-FPVGACLATAEAASGMVPGVHGTTAGGNPLAMAVAIAAFDEIAKPETLTHAREV 305 Query: 313 GDRL---LKHLQQIESELIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQGNIIR 369 L L L +I E+RG+GL +G+ L + + + +L N +R Sbjct: 306 AQHLRAGLDRLAATHPGVISEIRGKGLLVGVRLVPNNRAFMAAAREQRLLVAGGGDNCVR 365 Query: 370 IAPPLVIDKDEIDEVI 385 + PPL + E D+++ Sbjct: 366 LLPPLTLTVAEADQIL 381 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: 342 Number of extensions: 13 Number of successful extensions: 6 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: 398 Length adjustment: 31 Effective length of query: 363 Effective length of database: 367 Effective search space: 133221 Effective search space used: 133221 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