Align Alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_094578795.1 CEV32_RS19735 alcohol dehydrogenase AdhP
Query= reanno::Cup4G11:RR42_RS34260 (342 letters) >NCBI__GCF_002252475.1:WP_094578795.1 Length = 344 Score = 541 bits (1393), Expect = e-158 Identities = 265/341 (77%), Positives = 294/341 (86%), Gaps = 2/341 (0%) Query: 1 MTAMMKAAVVREFGAPLTIDEVPVPQPGRGQIQVKIEASGVCHTDLHAAEGDWPVKPTLP 60 M MKAAVVREFG PLTIDEVP+PQPG GQIQV I+ASGVCHTDLHAAEGDWPVKP P Sbjct: 1 MAKTMKAAVVREFGKPLTIDEVPIPQPGDGQIQVAIQASGVCHTDLHAAEGDWPVKPNPP 60 Query: 61 FIPGHEGVGYVSAVGAGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQQNTGYSV 120 FIPGHEGVG+VSAVG GV VKEGDRVG+PWLY+ACG+C HCL GWETLCE+Q NTGYSV Sbjct: 61 FIPGHEGVGFVSAVGKGVKHVKEGDRVGIPWLYTACGHCVHCLGGWETLCEEQLNTGYSV 120 Query: 121 NGGYGEYVVADPNYVGLLPDSVGFVEIAPILCAGVTVYKGLKVTDTRPGQWVVISGIGGL 180 NGG+ +YVVADPN+VG LP ++ F EIAPILCAGVTVYKGLKVTDT+PG WVVISGIGGL Sbjct: 121 NGGFADYVVADPNFVGHLPKNIEFNEIAPILCAGVTVYKGLKVTDTKPGDWVVISGIGGL 180 Query: 181 GHVAVQYARAMGLRVAAVDIDDKKLELARKLGAEVTVNART-TDPVAFLQKEI-GGAHGA 238 GH+AVQYA+AMGL VAAVDIDDKKL+LAR+LGA VTVNA+T DP A+++KE GGA G Sbjct: 181 GHMAVQYAKAMGLNVAAVDIDDKKLDLARRLGATVTVNAKTHNDPAAYIKKETDGGAQGV 240 Query: 239 LVTAVSPKAFGQAIGMVRRGGTIALNGLPPGDFPTPIFDVVLKGITIRGSIVGTRSDLQE 298 LVTAVSPKAF QAIGM RGGTIALNGLP GDFP IF++VL G+T+RGSIVGTR DLQE Sbjct: 241 LVTAVSPKAFEQAIGMAARGGTIALNGLPAGDFPLSIFNMVLNGVTVRGSIVGTRLDLQE 300 Query: 299 SLDFAAHGAVKATVSTAPLEKINEIFTRMRAGDIEGRVVMD 339 S+DFAA G VKAT+ T ++ IN IF MRAG IEGRVVMD Sbjct: 301 SIDFAADGKVKATIRTDKIDNINAIFDEMRAGQIEGRVVMD 341 Lambda K H 0.319 0.138 0.420 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: 464 Number of extensions: 13 Number of successful extensions: 2 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: 342 Length of database: 344 Length adjustment: 29 Effective length of query: 313 Effective length of database: 315 Effective search space: 98595 Effective search space used: 98595 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: 49 (23.5 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