Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate RR42_RS24700 RR42_RS24700 glucose-methanol-choline oxidoreductase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Cup4G11:RR42_RS24700 Length = 560 Score = 562 bits (1448), Expect = e-164 Identities = 280/524 (53%), Positives = 363/524 (69%), Gaps = 2/524 (0%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 +FDY++VG GS GCV+A RLS DP+++VC+LEAG ++ P G A++PTR NWA Sbjct: 4 QFDYIVVGGGSGGCVVAGRLSEDPNLSVCVLEAGGHGDGMVVKVPAGAVAMMPTRLNNWA 63 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 F T PQ GLGGR+GYQPRGK+LGGSS+IN M+YIRGH+ D++ W +LGN GW +DDVLPY Sbjct: 64 FDTVPQAGLGGRIGYQPRGKMLGGSSAINAMVYIRGHRSDYDRWASLGNSGWSYDDVLPY 123 Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPANRHAASEA-FVESALRAGHSYNPDFNGATQEGAG 180 FR SE + + +HG +G L VS +A ++E+A +AG DFNGA QEG G Sbjct: 124 FRLSEHNERFDNAWHGRNGPLNVSDLRTDNPFQARYLEAARQAGLPLTDDFNGAQQEGIG 183 Query: 181 YYDVTIRDGRRWSTATAFLKP-VRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239 Y VT + G RWS A A+L P + R+NLTV TH V I+L GK+A GV+ L G Sbjct: 184 IYQVTQKQGERWSAARAYLHPHIGRRANLTVETHAQVRRILLEGKRAVGVEVLQHGVIRT 243 Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299 LRAR+EV+L+AGA +P LLMLSG+G A EL GI LPGVG+NLQDH D V Y+ Sbjct: 244 LRARREVVLAAGALQTPQLLMLSGVGPAQELARVGIQTVQHLPGVGRNLQDHPDFVFGYR 303 Query: 300 SNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVI 359 + +G SL G V++ + + R R G + +N AE G FLKT P LE PDIQLH V+ Sbjct: 304 TGSLDTMGVSLLGSVRILSEILRFRRERRGMLTTNFAEGGGFLKTRPELEAPDIQLHFVV 363 Query: 360 GTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLK 419 VD+H R++ GHGFSCHVC+LRP+S GSV L S DP AP IDP F DV ++ Sbjct: 364 AMVDNHARRMRLGHGFSCHVCLLRPRSTGSVTLHSNDPLTAPLIDPAFFDDPLDVEDMVA 423 Query: 420 GYRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEMAV 479 G++ITR ++ +A + RD++++ + D+ + +LR+RTDT+YHP+GTC+MGQDEMAV Sbjct: 424 GFKITRRLMQTPALAKWATRDLFTSHVKTDDDIRAVLRQRTDTVYHPVGTCRMGQDEMAV 483 Query: 480 VDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 VD QLRVHG++GLRVVDASIMPTL+GGNTNA IMI E+A + I Sbjct: 484 VDPQLRVHGLDGLRVVDASIMPTLIGGNTNAPTIMIGEKAVDLI 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: 908 Number of extensions: 42 Number of successful extensions: 3 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: 560 Length adjustment: 35 Effective length of query: 491 Effective length of database: 525 Effective search space: 257775 Effective search space used: 257775 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