Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate Ga0059261_3205 Ga0059261_3205 transaminase, acetylornithine/succinylornithine family
Query= curated2:Q4A0N2 (394 letters) >FitnessBrowser__Korea:Ga0059261_3205 Length = 398 Score = 229 bits (583), Expect = 1e-64 Identities = 134/380 (35%), Positives = 205/380 (53%), Gaps = 9/380 (2%) Query: 16 YSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRA 75 Y ++ +G G + Y+D +G +V GH HP+ KA+ EQ+ + VS Sbjct: 10 YPRCEVRPVRGEGCYLIGERGERYLDFAAGIAVNALGHGHPQFTKAIAEQAATLMHVSNL 69 Query: 76 LYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMN 135 S ++I + + V N+G EA+E AIK AR++ N + ++I Sbjct: 70 YGSPQGEALAQRIVDNSFADTVFFTNSGVEAIECAIKTARRY--HYVNGNPQRHKLITFK 127 Query: 136 GNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQGE 195 FHGR++G++S + Q + GF PLL Y F D+E I+++T ++E +QGE Sbjct: 128 NAFHGRSIGAISATDQPKMRDGFEPLLPGFDYVKFNDLEGAIAKIDDETAGFLVETVQGE 187 Query: 196 GGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLG 255 GG+ FIQ +R+ C+E+ +LLI DEIQ G GRTGKM+A E PDI K +G Sbjct: 188 GGMTAGTVEFIQGLRKACDEHGLLLILDEIQCGYGRTGKMWAYEHYGITPDILTAAKGIG 247 Query: 256 GGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDR 315 G +P+ A LA ++ +T GTHGST+GGNPLA A A LDV+ E ++ +G+R Sbjct: 248 NG-FPLGACLATEEAAKGMTFGTHGSTYGGNPLAMAAGQAVLDVMLEPGFFEHVEKMGER 306 Query: 316 LLKHLQQI---ESELIVEVRGRGLFIGIELN--VAAQDYCEQM-INKGVLCKETQGNIIR 369 L +Q+ L E+RG+GL +GI+L ++D+ + N G+L N+ R Sbjct: 307 LRAGFEQLIPNHDHLFDEIRGKGLMLGIKLKEPAVSRDFVAHLRENHGLLTVAAGENVFR 366 Query: 370 IAPPLVIDKDEIDEVIRVIT 389 + PPLVI++ I E I ++ Sbjct: 367 VLPPLVIEESHIAECIEKLS 386 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: 393 Number of extensions: 25 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: 398 Length adjustment: 31 Effective length of query: 363 Effective length of database: 367 Effective search space: 133221 Effective search space used: 133221 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