Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 3607390 Dshi_0804 glucose-methanol-choline oxidoreductase (RefSeq)
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Dino:3607390 Length = 540 Score = 476 bits (1226), Expect = e-139 Identities = 250/528 (47%), Positives = 331/528 (62%), Gaps = 6/528 (1%) Query: 1 MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNW 60 ME DY+++GAGSAGCV+ANRLS D V LLEAGP D +P IH P+G + V+W Sbjct: 1 MEADYVVIGAGSAGCVVANRLSTDARNKVVLLEAGPPDTNPWIHIPVGYFKTMHNPTVDW 60 Query: 61 AFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLP 120 +KT PGL GR PRGKVLGGSSS+NG++Y+RG +D++ W+ +GN GWG+DDVLP Sbjct: 61 CYKTQADPGLNGRSIDWPRGKVLGGSSSLNGLLYVRGQPEDYDRWRQMGNAGWGWDDVLP 120 Query: 121 YFRKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGA 179 FR++E + G+ +HG DG L VS + +A+V +A G+ +NPD+NGA+QEG Sbjct: 121 LFRRAEANERGADPWHGDDGPLAVSNMRIQRPICDAWVAAAQAMGYPFNPDYNGASQEGV 180 Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239 GY+ +T R+GRR S A A+LKP R R NL+++T V I + GK+ TGV G R H Sbjct: 181 GYFQLTTRNGRRCSAAVAYLKPARKRPNLSIITRALVTRIEMEGKRVTGVTYTDAGGRAH 240 Query: 240 -LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCY 298 + AR+EVILS GA SPH+LMLSGIG +L+ GI PRH LPGVG+NLQDH L + Sbjct: 241 TVSARREVILSGGAINSPHILMLSGIGDPDQLQAHGITPRHALPGVGKNLQDHLQARLVF 300 Query: 299 KSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSV 358 K N+ + L + V + YA R GP+ + A FLKT P + PDIQ H Sbjct: 301 KCNEPT-LNDEVRSLVNQARIALKYALFRAGPMTMAASLATGFLKTRPDIATPDIQFHVQ 359 Query: 359 IGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLL 418 + D +H F+ VC LRP+S G + LA PDPR P I PN+L+ + D ATL Sbjct: 360 PWSADSPGEGVHPFSAFTMSVCQLRPESRGEIRLAGPDPRTYPTIHPNYLSTETDCATLT 419 Query: 419 KGYRITRDIIAQTPMA---SFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQD 475 +G +I R I P+A + R + L +D ++ R + +IYHP GTCKMG Sbjct: 420 EGVKIARRIARADPLAGKIAEEFRPPANLALDDDAATLDWARSNSVSIYHPTGTCKMGTG 479 Query: 476 EMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 AVVD++LRVHG+ GLRV D SIMP +V GNTNA AIMI E+ ++ + Sbjct: 480 PGAVVDARLRVHGLSGLRVADCSIMPEIVSGNTNAPAIMIGEKLSDMV 527 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: 822 Number of extensions: 34 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: 526 Length of database: 540 Length adjustment: 35 Effective length of query: 491 Effective length of database: 505 Effective search space: 247955 Effective search space used: 247955 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