Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate H281DRAFT_05794 H281DRAFT_05794 Choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Burk376:H281DRAFT_05794 Length = 550 Score = 514 bits (1323), Expect = e-150 Identities = 267/528 (50%), Positives = 351/528 (66%), Gaps = 5/528 (0%) Query: 1 MEFDYLIVGAGSAGCVLANRLSAD-PSVTVCLLEAGPE-DRSPLIHTPLGLAAILPTR-H 57 ME+DY+IVGAGS GC LA+RL+ D P T+ L+EAGP +R+ L++ P+G+AA++P + Sbjct: 1 MEYDYIIVGAGSGGCALASRLADDCPDATIALVEAGPHTNRNLLVNMPVGVAAVVPNKLK 60 Query: 58 VNWAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDD 117 N+ + TTPQPGL GR GYQPRG+ GGSS+IN MIY RGH D+++W G +GW + D Sbjct: 61 TNYGYLTTPQPGLAGRQGYQPRGRGFGGSSAINAMIYTRGHPLDYDEWAESGCDGWSWHD 120 Query: 118 VLPYFRKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQ 176 VLPYFR++E + G+ +HG G L VS R+ S FV++A+ AG+ N DFNG Q Sbjct: 121 VLPYFRRAEGNERGADAWHGDSGPLTVSDLRYRNPFSRRFVQAAIEAGYKPNDDFNGPDQ 180 Query: 177 EGAGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGS 236 EG G+Y VT RDGRR S A A++ R R+NL + V +V K+A GV+ + G Sbjct: 181 EGIGFYQVTQRDGRRCSVARAYVYD-RERANLHTIADATVLRVVFEQKRACGVEIVRGGR 239 Query: 237 RVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVL 296 R L+AR EV+++AGAF SP LLM SG+G AA L+ GI H+ P VGQNL DH D + Sbjct: 240 REMLKARAEVVVAAGAFNSPQLLMCSGVGPAAHLQAHGIEVLHDAPEVGQNLIDHVDFTI 299 Query: 297 CYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLH 356 + + GFS+ G +M + RH G ++SN AEAG FLK+ P LERPD+QLH Sbjct: 300 NKRVSSIEPTGFSVRGIGRMVPQFATFIRHGRGMLSSNVAEAGGFLKSKPTLERPDLQLH 359 Query: 357 SVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVAT 416 VDDHNR +HWGHG+S HVCVLRP S G+V LAS D R AP IDP F + D+ Sbjct: 360 FCAALVDDHNRHMHWGHGYSLHVCVLRPFSRGTVTLASADARAAPVIDPRFFSDSRDLDL 419 Query: 417 LLKGYRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDE 476 L++G ++ R I+ +A G R++Y+ D QL E + + DTIYHP+ TC+MG D Sbjct: 420 LVEGVQMARRILDAPSLALHGGRELYTRPGQTDAQLREAIARHADTIYHPVATCRMGGDA 479 Query: 477 MAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWIA 524 +VVD QLRV G+ GLR+VDAS+MPTL+GGNTNA +MI ERAAE IA Sbjct: 480 ASVVDPQLRVRGVTGLRIVDASVMPTLIGGNTNAPTVMIGERAAELIA 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: 884 Number of extensions: 48 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: 550 Length adjustment: 35 Effective length of query: 491 Effective length of database: 515 Effective search space: 252865 Effective search space used: 252865 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