Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate 199805 SO0617 acetylornithine aminotransferase (NCBI ptt file)
Query= curated2:Q5HJI8 (394 letters) >FitnessBrowser__MR1:199805 Length = 405 Score = 261 bits (667), Expect = 3e-74 Identities = 144/381 (37%), Positives = 221/381 (58%), Gaps = 9/381 (2%) Query: 15 NYAPLKLVISKGKGVKVWDTDGKQYIDCISGFSVANQGHCHPTIVKAMTEQASKLSIISR 74 NYAP ++ +G+G +VWD +G ++ID G +V GHCHP +V A+ Q KL +S Sbjct: 19 NYAPAAVIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHPALVNALKTQGEKLWHLSN 78 Query: 75 VLYSDNLGKWEEKICHLAKKDKVLPLNSGTEAVEAAIKIARKWGSEVKGITDGQVEIIAM 134 V+ ++ + K+ + ++V NSG EA EAA+K+AR++ E G+ EIIA Sbjct: 79 VMTNEPALELATKLVNSTFAERVYFANSGAEANEAALKLARRYALEKHGVEKD--EIIAF 136 Query: 135 NNNFHGRTLGSLSLSNHDAYKAGFHPLLQGTTTVDFGDIEQLTQAISPNTAAIILEPIQG 194 + FHGRT ++S+ AY GF P Q T + F D+ L A+S T AI+LEP+QG Sbjct: 137 DKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPFNDVAALEAAVSDKTCAIMLEPLQG 196 Query: 195 EGGVNIPPKGYIQAVRQLCDKHQILLIADEIQVGLGRTGKWFAMEWEQVVPDIYILGKAL 254 EGG+ +++AVR+L +KH L+I DE+Q G+GRTG+ +A +VPDI KAL Sbjct: 197 EGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELYAYMGTDIVPDILTTAKAL 256 Query: 255 GGGLYPVSAVLANNDVMRVLTPGTHGSTFGGNPLAIAISTAALDVLKDEQLVERSERLGS 314 GGG +P++A+L ++ L GTHGST+GGNPLA AI A LDV+ +++ + Sbjct: 257 GGG-FPIAAMLTTTEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNTPEVLNGVKHREQ 315 Query: 315 FLLKALLQL--KHPSIKEIRGRGLFIGIELNTD----AAPFVDQLIQRGILCKDTHRTII 368 L L ++ K+ E+RG+GL +G LN + F+ + G++ ++ Sbjct: 316 LLRDGLNKINEKYHVFSEVRGKGLLLGAVLNEQYQGRSRDFLVASVAEGLMSLMAGANVV 375 Query: 369 RLSPPLVIDKEEIHQIVAAFQ 389 R +P LVI + +I + +A F+ Sbjct: 376 RFAPSLVIPEADIAEGLARFE 396 Lambda K H 0.319 0.137 0.402 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: 369 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: 405 Length adjustment: 31 Effective length of query: 363 Effective length of database: 374 Effective search space: 135762 Effective search space used: 135762 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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