Align Alcohol dehydrogenase 2; EC 1.1.1.1; Alcohol dehydrogenase II; ADH II (uncharacterized)
to candidate 353293 BT3767 lactaldehyde reductase (NCBI ptt file)
Query= curated2:F8DVL8 (383 letters) >FitnessBrowser__Btheta:353293 Length = 384 Score = 305 bits (780), Expect = 2e-87 Identities = 166/357 (46%), Positives = 222/357 (62%), Gaps = 3/357 (0%) Query: 30 GFKNALIVSDAFMNKSGVVKQVADLLKTQGINSAVYDGVMPNPTVTAVLEGLKILKDNNS 89 GFK A V+D + K GV ++ + I +Y V NPT+ V G+ K + + Sbjct: 28 GFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYELYSDVKANPTIANVQNGVAAYKASGA 87 Query: 90 DFVISLGGGSPHDCAKAIALVATNG--GEVKDYEGIDKSKKPALPLMSINTTAGTASEMT 147 DF+++LGGGS D AK I +V N +VK EG+ +K A+P ++ TTAGTA+E+T Sbjct: 88 DFIVALGGGSSIDTAKGIGIVVNNPDFADVKSLEGVADTKHKAVPTFALPTTAGTAAEVT 147 Query: 148 RFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMVGMPKGLTAATGMDALTHAFEAYSSTA 207 +I DE KM VD + P V++ DP LM MPKGLTAATGMDALTHA E+Y + Sbjct: 148 INYVIIDEDARKKMVCVDPNDIPAVAIVDPELMYSMPKGLTAATGMDALTHAIESYITPG 207 Query: 208 ATPITDACALKAASMIAKNLKTACDNGKDMPAREAMAYAQFLAGMAFNNASLGYVHAMAH 267 A ++D LKA MIA+NLK A DNGKD AREAM+ AQ++AGM F+N LG VH+MAH Sbjct: 208 AWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAREAMSQAQYIAGMGFSNVGLGIVHSMAH 267 Query: 268 QLGGYYNLPHGVCNAVLLPHVLAYNA-SVVAGRLKDVGVAMGLDIANLGDKEGAEATIQA 326 LG +Y+ PHGV NA+LLP+V+ YNA S A + + AMG++ + + EG +A I+A Sbjct: 268 PLGAFYDTPHGVANALLLPYVMEYNAESPAAPKYIHIAKAMGVNTDGMTETEGVKAAIEA 327 Query: 327 VRDLAASIGIPANLTELGAKKEDVPLLADHALKDACALTNPRQGDQKEVEELFLSAF 383 V+ L+ SIGIP L E+ K+ED+P LA A D C NPR E+E L+ AF Sbjct: 328 VKALSLSIGIPQKLHEINVKEEDIPALAVAAFNDVCTGGNPRPTSVAEIEVLYRKAF 384 Lambda K H 0.316 0.132 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: 375 Number of extensions: 16 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 (21.6 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