Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate BWI76_RS26000 BWI76_RS26000 aspartate aminotransferase family protein
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Koxy:BWI76_RS26000 Length = 406 Score = 270 bits (691), Expect = 4e-77 Identities = 143/385 (37%), Positives = 223/385 (57%), Gaps = 9/385 (2%) Query: 16 YSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRA 75 Y+P + KG+G++VWD + Y+D G +V GHCHP ++ AL EQ +++ S Sbjct: 21 YAPAEFIPVKGKGSRVWDQQGKEYVDFAGGIAVTALGHCHPALVAALHEQGEKLWHTSNV 80 Query: 76 LYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMN 135 ++ + K+ + V+ MN+GTEA ETA K+AR + + ++IIA + Sbjct: 81 FTNEPALRLGRKLVDATFADRVVFMNSGTEANETAFKLARHY--TVTRHSPYKTKIIAFH 138 Query: 136 GNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQGE 195 FHGR+L ++S+ Q Y GFGP +I + F D+ +K ++++ T A+++EPIQGE Sbjct: 139 NAFHGRSLFTVSVGGQPKYSDGFGPKPADIVHVPFNDLHAVKAVMDDHTCAVVVEPIQGE 198 Query: 196 GGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLG 255 GGV F+Q +R LC+++ LL+ DE+Q G+GRTG +FA PDI K+LG Sbjct: 199 GGVTAATPEFLQGLRDLCDQHQALLVFDEVQCGMGRTGSLFAYMHYGVTPDILTSAKALG 258 Query: 256 GGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDR 315 GG +PISA+L D+ S G+HGST+GGNPLACAV AA D++N ++ + Sbjct: 259 GG-FPISAMLTTHDIASAFHAGSHGSTYGGNPLACAVGGAAFDLINTPEVLDGVTAKREL 317 Query: 316 LLKHLQQIES--ELIVEVRGRGLFIGIEL----NVAAQDYCEQMINKGVLCKETQGNIIR 369 ++HLQQI++ +L ++RG GL IG EL + A+D+ GV+ +++R Sbjct: 318 FVQHLQQIDARFDLFSDIRGMGLLIGAELKPQYHGKARDFLYAAAEAGVMVLNAGPDVMR 377 Query: 370 IAPPLVIDKDEIDEVIRVITEVLEK 394 P LVID +I E + + +E+ Sbjct: 378 FVPSLVIDDSDIAEGMARFAQAVER 402 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: 341 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: 406 Length adjustment: 31 Effective length of query: 363 Effective length of database: 375 Effective search space: 136125 Effective search space used: 136125 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