Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate Echvi_3848 Echvi_3848 Ornithine/acetylornithine aminotransferase
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Cola:Echvi_3848 Length = 381 Score = 186 bits (472), Expect = 1e-51 Identities = 119/383 (31%), Positives = 199/383 (51%), Gaps = 20/383 (5%) Query: 16 YSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRA 75 Y + + K G+ +WD + N Y+D G +V++ GH HP K ++EQ I S + Sbjct: 7 YPLIDVTPVKASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNIAFYSNS 66 Query: 76 LYSDNLGKWEEKICKLANKEN--VLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIA 133 + + K+ +L+ + + N+G EA E A+K+A + + IA Sbjct: 67 VQIPIQKELATKLGQLSGYPDYDLFLCNSGAEANENALKLA--------SFETGKKGFIA 118 Query: 134 MNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTA-IILEPI 192 FHGRT G+++L+ F +H F D+E ++K + T A +I+E I Sbjct: 119 FTKGFHGRTSGAVALTDNPKIIAPFNAH-EGVHILPFNDLEAVEKQLATGTIAGVIVEGI 177 Query: 193 QGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEW-ENTEPDIYLLG 251 QG GG+ +P F+ + L +Y LI DE+Q G R+GK FA +W E +PD+ + Sbjct: 178 QGVGGIQVPDPAFLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVEGLKPDLITVA 237 Query: 252 KSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALD 311 K +G G +PI VL + + + + G G+TFGGN LACA ++A L+V++EE+L+ A + Sbjct: 238 KGMGNG-FPIGGVLISPEFKA--SHGLLGTTFGGNHLACAAALAVLEVIDEENLITAAAE 294 Query: 312 LGDRLLKHLQQIESELIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQG--NIIR 369 G ++ L+++ + EVRG+GL IG +L A +I++ + + G + IR Sbjct: 295 NGKAIMAALEKVAG--VTEVRGKGLMIGFDLATEAGPVRAALIHEHKIFTGSAGGKHTIR 352 Query: 370 IAPPLVIDKDEIDEVIRVITEVL 392 + PPL I+ + + + VL Sbjct: 353 LLPPLNIEPKALTLFLEKLETVL 375 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: 346 Number of extensions: 22 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: 381 Length adjustment: 30 Effective length of query: 364 Effective length of database: 351 Effective search space: 127764 Effective search space used: 127764 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