Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_043920380.1 jaqu_RS17910 alcohol dehydrogenase catalytic domain-containing protein
Query= BRENDA::D4GSN2 (353 letters) >NCBI__GCF_000877395.1:WP_043920380.1 Length = 344 Score = 271 bits (692), Expect = 2e-77 Identities = 157/351 (44%), Positives = 204/351 (58%), Gaps = 12/351 (3%) Query: 1 MRAAVLREHGEPLDVTEVPDPTCDADGVVVEVEACGICRSDWHSWMGHGEWADDAVPSGQ 60 MRAA+LR + EPL + +VP P C DGVV++V ACG+CRSDWH W+G V GQ Sbjct: 1 MRAAILRTYHEPLAIEDVPHPDCPPDGVVLKVLACGVCRSDWHGWVGE----HPRVKPGQ 56 Query: 61 ILGHEPAGRVVEAGDRVETIREGDRVALPFNLACGSCGYCQTGHGNVCTGDHPHALGFEP 120 I GHE G VVEAG + T GD + PF LACG+C C++G N C EP Sbjct: 57 IGGHEYCGEVVEAGPQA-THAVGDLLIAPFILACGTCPQCRSGAQNTCLDQRLPGF-IEP 114 Query: 121 AAQGAFAELVHLPSADYNAIQLPEDVLPTDVAALGCRFMTAYNALDARAGLRAGQWVAVH 180 GAFAE V +P D+N +LPE + PT AALGCR TA++AL RA L G+W+AVH Sbjct: 115 ---GAFAEYVAVPR-DHNLARLPEGMAPTLAAALGCRVTTAWHALTGRAALAGGEWLAVH 170 Query: 181 GCGGVGLSTIQVANVLGARVVAVDVRESALDAAADLGADAVVDGSAEDPVDAIRGLTDGG 240 G GG+GLS + LGARVV VDV + LD A LG D+ V + ED IR +T GG Sbjct: 171 GTGGIGLSAALLGRALGARVVVVDVVQEKLDHALSLGIDSAV-MAGEDTAARIREITGGG 229 Query: 241 AHVSLDALGVAETCRNSVRSVRPRGSHVQVGLTTEAEKGNVSLPTDWMTRHEVSFLGARG 300 AHVS++ALG+ T S+ +RP G HVQVG+ + + + + ++ G RG Sbjct: 230 AHVSVEALGIPATVNASLECLRPLGRHVQVGMPV-GHTARMEVDMSAVYQGNLALFGTRG 288 Query: 301 MPPTNADDLLSLLASDAVDPGSLVTKTVSLDEVPERLAAMTDYDTVGVEVM 351 MP LL+L+ S AVD ++ + V+L +V LAA GV V+ Sbjct: 289 MPSWRYSSLLALIESGAVDLAPMIAREVALSDVSAELAAFDGPTPPGVAVI 339 Lambda K H 0.317 0.134 0.412 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: 442 Number of extensions: 27 Number of successful extensions: 6 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: 353 Length of database: 344 Length adjustment: 29 Effective length of query: 324 Effective length of database: 315 Effective search space: 102060 Effective search space used: 102060 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 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