Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate BPHYT_RS18735 BPHYT_RS18735 GMC family oxidoreductase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__BFirm:BPHYT_RS18735 Length = 552 Score = 509 bits (1310), Expect = e-148 Identities = 264/528 (50%), Positives = 349/528 (66%), Gaps = 5/528 (0%) Query: 1 MEFDYLIVGAGSAGCVLANRLSAD-PSVTVCLLEAGPE-DRSPLIHTPLGLAAILPTR-H 57 M++DY+IVGAGS GC LA+RL+ P T+ L+EAGP DR+ ++ P+G+AA++P + Sbjct: 1 MQYDYIIVGAGSGGCALASRLADSCPDATIALIEAGPHTDRNLFVNMPVGVAAVVPHKLK 60 Query: 58 VNWAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDD 117 N+ + TTPQPGLGGR GYQPRG+ GGSS+IN MIY RGH D+++W LG EGW + + Sbjct: 61 TNYGYLTTPQPGLGGRQGYQPRGRGFGGSSAINAMIYTRGHPLDYDEWAELGCEGWSWTE 120 Query: 118 VLPYFRKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQ 176 VLPYFR++E + G+ +HG G L VS ++ S FV++A+ AG+ N DFNGA Q Sbjct: 121 VLPYFRRTEGNQRGADAWHGDSGPLTVSDLRYQNPFSRRFVQAAIEAGYKPNSDFNGADQ 180 Query: 177 EGAGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGS 236 EG G+Y VT RDGRR S A A++ R R NL + V + GK+A+GV+ + G Sbjct: 181 EGIGFYQVTQRDGRRCSVARAYIYD-RARPNLHTIADATVLRVAFNGKRASGVEIVRGGR 239 Query: 237 RVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVL 296 L AR EV+L+AGAF SP LLM SGIG AA L+ GIA H+ P VGQNL DH D + Sbjct: 240 TETLEARAEVVLAAGAFNSPQLLMCSGIGPAAHLQSLGIAVLHDAPEVGQNLIDHVDFTI 299 Query: 297 CYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLH 356 + + GFS+ G +M + RH G ++SN AEAG FLK+ P L+RPD+QLH Sbjct: 300 NKRVSSIEPTGFSIRGIARMLPQFVTFMRHGRGMLSSNVAEAGGFLKSKPTLDRPDLQLH 359 Query: 357 SVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVAT 416 VDDHNR +HWGHG+S HVCVLRP S G+V LAS D R AP IDP F + D+ Sbjct: 360 FCAAIVDDHNRHMHWGHGYSLHVCVLRPHSRGTVTLASADARTAPVIDPRFFSDPRDLDL 419 Query: 417 LLKGYRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDE 476 L+ G R+ R I+ +A G ++Y+ +D +L + + DTIYHP+ TC+MG D Sbjct: 420 LVDGARMARRILDAPSLALHGGSELYTHSGQSDAELRRTIVEHADTIYHPVATCRMGGDA 479 Query: 477 MAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWIA 524 +VVD QLRV G+ GLR+VDAS+MPTL+GGNTN+ +MI ERAA+ IA Sbjct: 480 RSVVDPQLRVRGVTGLRIVDASVMPTLIGGNTNSPTVMIGERAADLIA 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: 879 Number of extensions: 48 Number of successful extensions: 6 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: 552 Length adjustment: 35 Effective length of query: 491 Effective length of database: 517 Effective search space: 253847 Effective search space used: 253847 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