Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_015943022.1 DHAF_RS03890 aspartate aminotransferase family protein
Query= curated2:Q4A0N2 (394 letters) >NCBI__GCF_000021925.1:WP_015943022.1 Length = 399 Score = 290 bits (743), Expect = 4e-83 Identities = 153/378 (40%), Positives = 224/378 (59%), Gaps = 5/378 (1%) Query: 16 YSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRA 75 Y L +A+ KG+G VWDIE Y+D ++G +V + GH HP +++A+Q+Q++ I S Sbjct: 20 YGRLPMAIVKGKGTTVWDIEGKQYLDFVTGLAVSSLGHSHPAVVEAIQKQAEEILHTSNL 79 Query: 76 LYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMN 135 + N EK+ + + + V N+G EA E AIK+ARK+ + + E EI+ + Sbjct: 80 YWIPNQIALAEKLVEHSFADQVFFCNSGAEANEAAIKIARKYAKE--HYSEDKYEILTLV 137 Query: 136 GNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQGE 195 +FHGRTL +L+ + Q Y+KG+ PL Y D+ QL++ +N + A++LEPIQGE Sbjct: 138 NSFHGRTLATLTATGQTKYQKGYAPLPEGFTYVPINDLAQLEEKMNPKVAAVMLEPIQGE 197 Query: 196 GGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLG 255 GGV F+ + R+LC++Y LLI DEIQVGLGRTGK+FA EW N PDI L K+LG Sbjct: 198 GGVFPLEVEFLAKARKLCDDYGALLIFDEIQVGLGRTGKLFAYEWSNVVPDIMTLAKALG 257 Query: 256 GGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDR 315 GG+ PI +LA + V S PG H STFGGNPLA AV A +DVL EE +++ Sbjct: 258 GGV-PIGVMLAKEKVASTFKPGDHASTFGGNPLATAVGCAVMDVLTEEGFLEDVQKRAQY 316 Query: 316 LLKHLQQI--ESELIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQGNIIRIAPP 373 + LQ++ + + E+RG+G +G L+ + E KG+L G +R PP Sbjct: 317 FKQELQKLADKYQTGTEIRGQGFILGWPLDRLGAEIVEGAREKGLLINFVGGKALRFLPP 376 Query: 374 LVIDKDEIDEVIRVITEV 391 L + EIDE I ++ ++ Sbjct: 377 LNVSYQEIDEAITILDQI 394 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: 387 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: 399 Length adjustment: 31 Effective length of query: 363 Effective length of database: 368 Effective search space: 133584 Effective search space used: 133584 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