Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_002879650.1 B506_RS06460 aldo/keto reductase
Query= BRENDA::Q8TZM9 (278 letters) >NCBI__GCF_000387565.1:WP_002879650.1 Length = 285 Score = 130 bits (328), Expect = 2e-35 Identities = 96/266 (36%), Positives = 139/266 (52%), Gaps = 31/266 (11%) Query: 17 KVTAIGMGTWGIGGRETPDYSRDKESIEAIRYGLELGMNLIDTAEFYGAGHAEEIVGEAI 76 K+ IG GTW +TPD +E++E L G IDTA YG E VG AI Sbjct: 17 KIPVIGFGTW-----QTPDGDVAQEAVET---ALNAGYRHIDTAAVYGN---EASVGRAI 65 Query: 77 KE--FEREDIFIVSKVWPTHFGYEEAKKAARASAKRLGT-YIDLYLLHWP----VDDF-- 127 K +R D+F+ SK+W YE AK A S +L T Y+DLYL+HWP + D Sbjct: 66 KRSGVKRSDLFVTSKLWNGSHSYEGAKAAIDDSLLKLDTDYLDLYLIHWPNPVAIRDHWA 125 Query: 128 KKIEETLHALEDLVDEGVIRYIGVSNF---NLELLQRSQEVMRKYEIVANQVKYSVKDRW 184 + E A+E+ V G IR IGVSNF +LE L ++ E+ + V NQ+ + D Sbjct: 126 EGNAEAWRAMEEAVQAGKIRAIGVSNFRRHHLEALLKTAEI----KPVVNQICLNPNDLQ 181 Query: 185 PETTGLLDYMKREGIALMAYTPLEKGTLARNECLAKIGEKYGKTAAQVALNYLIWEENVV 244 E T K G+ AY+PL G L NE + +G KYGK++AQV + + + + N + Sbjct: 182 AEVTAA---NKEYGLLSEAYSPLGTGGLLGNETIKAVGAKYGKSSAQVLIRWSL-QHNFL 237 Query: 245 AIPKASNKEHLKENFGAMGWRLSEED 270 +PK+ + +++K N + L+ +D Sbjct: 238 PLPKSVHPDYIKANAEVFDFALTADD 263 Lambda K H 0.317 0.136 0.400 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: 222 Number of extensions: 19 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: 278 Length of database: 285 Length adjustment: 26 Effective length of query: 252 Effective length of database: 259 Effective search space: 65268 Effective search space used: 65268 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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