Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Echvi_3219 Echvi_3219 Zn-dependent alcohol dehydrogenases
Query= BRENDA::Q8L3C9 (344 letters) >FitnessBrowser__Cola:Echvi_3219 Length = 343 Score = 531 bits (1368), Expect = e-155 Identities = 250/341 (73%), Positives = 295/341 (86%) Query: 1 MLPKTMKAAVIREFGSLLKIEEVEVKRPGRNEILVKVIASGVCHTDLHAVEGDWPVKPKM 60 MLPKTMKAAV+ EFG LKIEE+ VK P N+ILV+V+ASGVCHTDLHA +GDWPVKP++ Sbjct: 1 MLPKTMKAAVVTEFGQPLKIEEIPVKAPNENQILVQVMASGVCHTDLHAADGDWPVKPRL 60 Query: 61 PLIPGHEAVGYVVAVGQEVKNVKEGDAVGVPWLYSACGGCDQCITGWETLCDTQQNGGYS 120 PLIPGHE +GYV AVG VKN KEGD VGVPWLYSACG C+ CITGWETLC++Q NGGYS Sbjct: 61 PLIPGHEGIGYVAAVGSNVKNTKEGDIVGVPWLYSACGHCEHCITGWETLCESQVNGGYS 120 Query: 121 VDGGFAEYVIADARYVGLLPSNVNFMEMAPILCAGVTVYKGLKETEVKPGEWVAISGIGG 180 VDGG+AEYV+AD YVG ++F++MAPILCAGVTVYKGLKETEV+PG+WVAISGIGG Sbjct: 121 VDGGYAEYVLADPNYVGRFSGAIDFVQMAPILCAGVTVYKGLKETEVRPGQWVAISGIGG 180 Query: 181 LGHVAVQYAKAMGMHVAAIDVADDKLDLAKKLGADLVVNAKNQNPGEFLKKEVGGMHGAL 240 LGHVAVQYAKAMG+HV A+DV+DDKL+LAKKLGAD VVN KN + +KE GG+HG L Sbjct: 181 LGHVAVQYAKAMGLHVLAVDVSDDKLNLAKKLGADRVVNGKNPDEVMNARKETGGVHGVL 240 Query: 241 ITAVSPIAFKQGLETLRRKGTMALNGLPPGNFDLSIFDTVLNRITIRGSIVGTRKDMKEA 300 +TAVSP+AF+Q L+ LRRKGT+ +NGLPPG+FDL IF+TVLNR T+RGSIVGTRKD++EA Sbjct: 241 VTAVSPVAFRQALDLLRRKGTLVMNGLPPGSFDLPIFETVLNRYTVRGSIVGTRKDLQEA 300 Query: 301 IEFAVEGKVKATVTPAKLENINEVFDKMKKGQIEGRVVLEI 341 I+FA+EGKV TV A LE+IN +FD+MKKGQIEGR+VL+I Sbjct: 301 IDFAMEGKVTTTVKSAPLEDINLIFDQMKKGQIEGRMVLDI 341 Lambda K H 0.318 0.137 0.404 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: 467 Number of extensions: 16 Number of successful extensions: 1 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: 344 Length of database: 343 Length adjustment: 29 Effective length of query: 315 Effective length of database: 314 Effective search space: 98910 Effective search space used: 98910 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 (21.7 bits) S2: 49 (23.5 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