Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 3608021 Dshi_1428 glucose-methanol-choline oxidoreductase (RefSeq)
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Dino:3608021 Length = 544 Score = 301 bits (772), Expect = 3e-86 Identities = 198/531 (37%), Positives = 274/531 (51%), Gaps = 42/531 (7%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 E+D++++G GSAG +L A + +LEAG D +H AA L T W Sbjct: 45 EYDFIVIGTGSAGAACVYQL-AQTGARILVLEAGRNDDLEEVHDSRLWAASLGTDATKW- 102 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 F+T P GR PRG VLGG+S++N M+Y RGH+ DF+ W+ +G GW ++DVLP+ Sbjct: 103 FETLPSSHTDGRNHMWPRGNVLGGTSALNAMVYARGHRTDFDVWETMGATGWSYEDVLPH 162 Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPA---NRHAASEAFVESALRAGHSYNPDFNGATQEG 178 F E + G E G G ++VS +RH + AF+++A G+ P FN G Sbjct: 163 FMAMESYEPGG-ENRGTSGPIFVSQPQDPHRHEGAVAFMDAAAGLGYKETPSFNSDRMSG 221 Query: 179 AGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRV 238 + D I+D RR S+A AFL+P N+T+LT V+ + L G + TGV L G+ V Sbjct: 222 QAWIDFNIKDQRRQSSAVAFLRPAIENGNITLLTDAPVQKLTLEGTKCTGVTYLHNGAPV 281 Query: 239 HLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCY 298 +RA EVILSAGA SP LLMLSGIG A++L GI +LP VG LQDH Sbjct: 282 SVRAANEVILSAGAIDSPRLLMLSGIGIASDLRQVGIDAVVDLP-VGVGLQDH------- 333 Query: 299 KSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVA---SNCAEAGAFLKTDPGLERPDIQL 355 +LG ++ K GPV N +E + ++DPGL PD+ Sbjct: 334 ------ILGAGVNYEAK-------------GPVPVSHYNHSEVYMWERSDPGLRSPDMIA 374 Query: 356 HSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVA 415 V KL + HG+ V P+S G V LAS D AP I+ N+LA + D Sbjct: 375 LYVSVPFASTGHKLDYEHGYCILSGVATPQSRGYVKLASDDIADAPIIETNYLAEEQDWK 434 Query: 416 TLLKGYRITRDIIAQTPMASFGLRDM--YSAGLHNDEQLIELLRKRTDTIYHPIGTCKMG 473 + + R++ A A F R+ G D + + L +T +HP TC++G Sbjct: 435 SYRAATELCRELGASDAYAEFRKRESLPQKDGELTDAEWRDFLSASVNTYFHPTSTCQIG 494 Query: 474 QDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWIA 524 + VV+ LRV GIEGLRV DAS+MP + NTNA +MI RA + I+ Sbjct: 495 K----VVEPDLRVKGIEGLRVADASVMPQITTSNTNAPTMMIGWRAGDMIS 541 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: 744 Number of extensions: 43 Number of successful extensions: 8 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: 544 Length adjustment: 35 Effective length of query: 491 Effective length of database: 509 Effective search space: 249919 Effective search space used: 249919 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