Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_090273343.1 BLU11_RS10765 aspartate aminotransferase family protein
Query= curated2:Q4A0N2 (394 letters) >NCBI__GCF_900105005.1:WP_090273343.1 Length = 404 Score = 269 bits (687), Expect = 1e-76 Identities = 143/383 (37%), Positives = 231/383 (60%), Gaps = 9/383 (2%) Query: 9 DKYSSKNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQR 68 D+ NY+P+++ +G G+++WD + YID G +V + GH HP++++AL EQ+Q+ Sbjct: 13 DRLMVPNYAPVEMIPVRGDGSRLWDQQGREYIDLAGGIAVNSLGHAHPQLVEALTEQAQK 72 Query: 69 ITMVSRALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESS 128 + VS + ++ + +K+ + VL +N+G EA E A K+AR+W D D+ Sbjct: 73 LWHVSNIMTNEPALRLADKLVAATFADKVLFVNSGAEANEAAFKLARRWAHDQSGPDKH- 131 Query: 129 SEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAII 188 EIIA + +FHGRTL ++S+ Q Y +GFGP ++ I + + DI L+ I+ +T A++ Sbjct: 132 -EIIACSNSFHGRTLFTVSVGGQPKYSQGFGPAISGISHVPYNDIAALEAQISERTCAVV 190 Query: 189 LEPIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIY 248 +EP+QGEGGV +++ VR LC++YN LLI DE+Q G+GRTGK++A PDI Sbjct: 191 VEPVQGEGGVIPASIEYLKAVRALCDKYNALLIFDEVQSGMGRTGKLYAYMHSGVAPDIL 250 Query: 249 LLGKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQN 308 K +GGG +PI+A+L V L+ GTHGST+GGNPL CAV+ LD++N ++ Sbjct: 251 TSAKGIGGG-FPIAAMLTIDRVAPALSVGTHGSTYGGNPLGCAVAERVLDIINTPQVLDG 309 Query: 309 ALDLGDRLLKHLQQIESELIV--EVRGRGLFIGIELNVAAQDYCEQMI----NKGVLCKE 362 + +L L+ + EL V E+RG+GL IG L + Q++ +G+L + Sbjct: 310 VGERQAQLTAGLRILADELGVFSEIRGQGLLIGAVLAERWRGQAGQVMRLAQEEGLLVLQ 369 Query: 363 TQGNIIRIAPPLVIDKDEIDEVI 385 +++R+AP L+I + +I E + Sbjct: 370 AGADVVRLAPSLIIPEADIREAL 392 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: 343 Number of extensions: 13 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: 404 Length adjustment: 31 Effective length of query: 363 Effective length of database: 373 Effective search space: 135399 Effective search space used: 135399 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 24 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