Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate SMc04390 SMc04390 L-sorbose dehydrogenase, FAD dependent protein
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Smeli:SMc04390 Length = 551 Score = 381 bits (979), Expect = e-110 Identities = 222/531 (41%), Positives = 310/531 (58%), Gaps = 15/531 (2%) Query: 1 MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHV-N 59 M +DY+I GAG AGCVLANRLS DP V V LLEAG D +PL H P G A + T+ V + Sbjct: 1 MTYDYIITGAGPAGCVLANRLSEDPDVRVLLLEAGGGDWNPLFHMPAGFAKM--TKGVAS 58 Query: 60 WAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQAL-GNEGWGFDDV 118 W + T PQ + GRV + KV+GG SSIN +Y RG+ D++ W + G GW + V Sbjct: 59 WGWHTVPQKHMKGRVLRYTQAKVIGGGSSINAQLYTRGNAADYDLWASEEGCAGWDYRSV 118 Query: 119 LPYFRKSEMHHGGSSEYHGGDGELYVS-PANRHAASEAFVESALRAGHSYNPDFNGATQE 177 LPYF+++E + + +YH G L VS P + +A++ + G YN DFNG Q Sbjct: 119 LPYFKRAEDNQRFADDYHSYGGPLGVSMPVSALPICDAYIRAGQELGIPYNHDFNGRQQA 178 Query: 178 GAGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALI-KGS 236 G G+Y +T R+ RR S + A+L P++ R NLTV T V I+L G++A GV+ + +GS Sbjct: 179 GVGFYQLTQRNRRRSSASLAYLSPIKDRPNLTVRTGARVARIMLEGRRAVGVEVVTGRGS 238 Query: 237 RVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVL 296 + +RA +EV++S+GA GSP LL+ SGIG A L G+ RH+LPGVG NLQDH D+ + Sbjct: 239 EI-IRADREVLVSSGAIGSPKLLLQSGIGPADHLRSVGVEVRHDLPGVGGNLQDHLDLFV 297 Query: 297 CYKSNDTSLLGFSLSGGVKMGKAMF---DYARHRNGPVASNCAEAGAFLKTDPGLERPDI 353 + + G ++ + ++ Y R+GPVAS+ E G F DP PDI Sbjct: 298 ISECTG----DHTYDGVARLHRTLWAGLQYVLFRSGPVASSLFETGGFWYADPNARSPDI 353 Query: 354 QLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDD 413 Q H +G+ + G + + L P+S G+V L+S DP AP IDPN+ D Sbjct: 354 QFHLGLGSGIEAGVARLKNAGVTLNSAYLHPRSRGTVRLSSADPAAAPLIDPNYWEDPHD 413 Query: 414 VATLLKGYRITRDIIAQTPMASFGLRD-MYSAGLHNDEQLIELLRKRTDTIYHPIGTCKM 472 L+G +I R+I+ Q + F L + + G+ DEQL + T +HP+GTCKM Sbjct: 414 RQMSLEGLKIAREIMQQPALKPFVLDERLPGNGIRTDEQLFDYGCANAKTDHHPVGTCKM 473 Query: 473 GQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 G D AVVD +L+V GIEGLRV D+S+MP + NTN IM+ E+ A+ I Sbjct: 474 GTDAAAVVDLELKVRGIEGLRVCDSSVMPRVPSCNTNGPTIMMGEKGADII 524 Lambda K H 0.319 0.137 0.419 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: 803 Number of extensions: 53 Number of successful extensions: 7 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: 526 Length of database: 551 Length adjustment: 35 Effective length of query: 491 Effective length of database: 516 Effective search space: 253356 Effective search space used: 253356 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: 52 (24.6 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