Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Btheta:353284 Length = 373 Score = 218 bits (555), Expect = 2e-61 Identities = 131/383 (34%), Positives = 215/383 (56%), Gaps = 22/383 (5%) Query: 16 YSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRA 75 Y + + KG+G KVWD Y+D G +V++ GH HP ++ + Q + S + Sbjct: 7 YPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSNS 66 Query: 76 LYSDNLGKWEEKICKLANKEN--VLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIA 133 + + + E++ K++ E+ + +N+G EA E A+K+A + K +I+ Sbjct: 67 VINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTK--------VIS 118 Query: 134 MNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIH--YADFGDIEQLKK-LINNQTTAIILE 190 + FHGRT ++ ++ + P+ NN H Y DIE +K+ L A+I+E Sbjct: 119 FSKAFHGRTSLAVEATNNPTI---IAPINNNGHVTYLPLNDIEAMKQELAKGDVCAVIIE 175 Query: 191 PIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLL 250 IQG GG+ IP T F+QE+R++C E +LI DEIQ G GR+GK FA ++ + +PDI + Sbjct: 176 GIQGVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITV 235 Query: 251 GKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNAL 310 K +G G +P++ VL + V G G+TFGGN LAC+ ++A +DV+ +++LV+NA Sbjct: 236 AKGIGNG-FPMAGVLISPMFKPVY--GQLGTTFGGNHLACSAALAVMDVIEQDNLVENAK 292 Query: 311 DLGDRLLKHLQQIESELIVEVRGRGLFIGIELNVAAQDYCEQMI-NKGVLCKETQGNIIR 369 +GD LL+ L++ I EVRGRGL IG+E ++ ++I ++ V + N++R Sbjct: 293 AVGDYLLEELKKFPQ--IKEVRGRGLMIGLEFEEPIKELRSRLIYDEHVFTGASGTNVLR 350 Query: 370 IAPPLVIDKDEIDEVIRVITEVL 392 + PPL + +E DE + VL Sbjct: 351 LLPPLCLSMEEADEFLARFKRVL 373 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: 381 Number of extensions: 14 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: 373 Length adjustment: 30 Effective length of query: 364 Effective length of database: 343 Effective search space: 124852 Effective search space used: 124852 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