Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate BPHYT_RS07695 BPHYT_RS07695 acetylornithine aminotransferase
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__BFirm:BPHYT_RS07695 Length = 411 Score = 239 bits (609), Expect = 1e-67 Identities = 129/384 (33%), Positives = 213/384 (55%), Gaps = 9/384 (2%) Query: 16 YSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRA 75 +SP +G G++VWD + YID G +V GH HP+++ L EQ ++ + Sbjct: 19 FSPAAFVPDRGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLNVLHEQGGKLWHIGNG 78 Query: 76 LYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMN 135 ++ + + +++ L + N+G EA E A+K+AR+ D D+ EII+ Sbjct: 79 YTNEPVLRLAKRLEDLTFADRAFFANSGAEANEAALKLARRVAFDRHGADKY--EIISFT 136 Query: 136 GNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQGE 195 +FHGRT ++S+ Q Y +GFGP+ I + + DIE +KK I QT A+I+EPIQGE Sbjct: 137 QSFHGRTFFTVSVGGQPKYSEGFGPVPAGITHLPYNDIEAVKKAIGAQTCAVIVEPIQGE 196 Query: 196 GGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLG 255 GGV F++ +R+ C+++ LLI DE+Q G+GR+G +A + PDI K+LG Sbjct: 197 GGVIPADPAFLKALREACDQHGALLIFDEVQTGVGRSGYFYAYQETGVTPDILTTAKALG 256 Query: 256 GGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDR 315 G +PI A+L ++ + G HG+T+GGNPL A++ ++++++ L++ + Sbjct: 257 NG-FPIGAMLTTNELAAYFKVGVHGTTYGGNPLGAAIAEKVVELVSDPKLLEGVRSRSEA 315 Query: 316 LLKHLQQIESE--LIVEVRGRGLFIGIELNVA----AQDYCEQMINKGVLCKETQGNIIR 369 L HL ++ L EVRGRGL IG ELN A A+D+ GV+ +++R Sbjct: 316 LKGHLAKLNERFGLFTEVRGRGLLIGAELNEAFKGRAKDFVTAAGQHGVIMLMAGPDVLR 375 Query: 370 IAPPLVIDKDEIDEVIRVITEVLE 393 P L++ D+++E + + +E Sbjct: 376 FVPSLIMPLDDMNEGFERLAKAIE 399 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: 350 Number of extensions: 12 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: 411 Length adjustment: 31 Effective length of query: 363 Effective length of database: 380 Effective search space: 137940 Effective search space used: 137940 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