Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 353293 BT3767 lactaldehyde reductase (NCBI ptt file)
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Btheta:353293 Length = 384 Score = 294 bits (753), Expect = 2e-84 Identities = 159/356 (44%), Positives = 218/356 (61%), Gaps = 3/356 (0%) Query: 30 GFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNC 89 GF + VTD L K G+A ++ K ++ +I +Y + NPT NV G+ K + Sbjct: 28 GFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYELYSDVKANPTIANVQNGVAAYKASGA 87 Query: 90 DSVISLGGGSPHDCAKGIALVAANG--GDIRDYEGVDRSAKPQLPMIAINTTAGTASEMT 147 D +++LGGGS D AKGI +V N D++ EGV + +P A+ TTAGTA+E+T Sbjct: 88 DFIVALGGGSSIDTAKGIGIVVNNPDFADVKSLEGVADTKHKAVPTFALPTTAGTAAEVT 147 Query: 148 RFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSLTAATGMDALTHAIEAYVSIA 207 +I DE KM VD + P +++ D LM MPK LTAATGMDALTHAIE+Y++ Sbjct: 148 INYVIIDEDARKKMVCVDPNDIPAVAIVDPELMYSMPKGLTAATGMDALTHAIESYITPG 207 Query: 208 ATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQFLAGMAFNNASLGYVHAMAH 267 A ++D LKA+ MIA+NL AV++G + AREAM+ AQ++AGM F+N LG VH+MAH Sbjct: 208 AWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAREAMSQAQYIAGMGFSNVGLGIVHSMAH 267 Query: 268 QLGGFYNLPHGVCNAVLLPHVQVFNSK-VAAARLRDCAAAMGVNVTGKNDAEGAEACINA 326 LG FY+ PHGV NA+LLP+V +N++ AA + A AMGVN G + EG +A I A Sbjct: 268 PLGAFYDTPHGVANALLLPYVMEYNAESPAAPKYIHIAKAMGVNTDGMTETEGVKAAIEA 327 Query: 327 IRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTNPIQATHEEIVAIYRAA 382 ++ L+ + IP L ++NVKEED LA A D C NP + EI +YR A Sbjct: 328 VKALSLSIGIPQKLHEINVKEEDIPALAVAAFNDVCTGGNPRPTSVAEIEVLYRKA 383 Lambda K H 0.318 0.131 0.373 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: 378 Number of extensions: 17 Number of successful extensions: 3 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: 383 Length of database: 384 Length adjustment: 30 Effective length of query: 353 Effective length of database: 354 Effective search space: 124962 Effective search space used: 124962 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 (21.8 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