Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate HSERO_RS24000 HSERO_RS24000 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__HerbieS:HSERO_RS24000 Length = 539 Score = 366 bits (939), Expect = e-105 Identities = 216/529 (40%), Positives = 297/529 (56%), Gaps = 12/529 (2%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 ++DY+I+GAG+AGCV+ANRLS V L+EAG +D IH P+G + +W Sbjct: 6 QYDYIIIGAGTAGCVMANRLSRKTGKKVLLIEAGAKDDYIWIHIPVGYLYCINNPRTDWM 65 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDW-QALGNEGWGFDDVLP 120 F+T GL GR PRGKVLGG SSINGMIY+RG D++ W G++ W + +VLP Sbjct: 66 FRTEADAGLNGRSLIYPRGKVLGGCSSINGMIYMRGQARDYDHWADVTGDDSWRWQNVLP 125 Query: 121 YFRKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGA 179 F+KSE +H G+ ++HG GE V R +AF ++A G DFN EG Sbjct: 126 LFKKSEDYHLGAGQFHGAGGEWRVEKQRLRWDILDAFRDAAAENGIPKVEDFNCGDNEGC 185 Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVL----LGKQATGVQALIKG 235 GY+DV + G RW+ + AFL+P NLT++T +HV + + G TGV+ G Sbjct: 186 GYFDVNQKRGVRWNASKAFLRPAMKDGNLTIMTGSHVSRLRMEQGEQGPVCTGVEFTGGG 245 Query: 236 SRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVV 295 S A KE IL AGA GSPH+L +SGI A L+ I H LPGVG+NLQDH + Sbjct: 246 SAWFAEA-KETILCAGAIGSPHILQMSGIADPALLQQHQIPVVHALPGVGENLQDHLQMR 304 Query: 296 LCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQL 355 + +K N L S V + Y ++GP++ ++ GAF K+D ++Q Sbjct: 305 MVFKVNGAKTLNAMASTLVGKMQIGLQYLFTQSGPMSMAPSQLGAFAKSDAQQASANLQY 364 Query: 356 HSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVA 415 H +++ LH F+ VC LRP S G V LAS D APRI N+L+ ++D+ Sbjct: 365 HVQPLSLEKFGDPLHAFPAFTASVCNLRPTSRGHVRLASGDHALAPRITTNYLSTEEDLK 424 Query: 416 TLLKGYRITRDIIAQTPMASFGLRDMYSAGLH--NDEQLIELLRKRTDTIYHPIGTCKMG 473 R+TR IA +P S + Y G H +E L + TI+HP+GTC+MG Sbjct: 425 VAANALRLTRR-IAASPALSRYRPEEYKPGAHYETEEDLYRAAGEVGTTIFHPVGTCRMG 483 Query: 474 Q--DEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAA 520 + D MAVVD+Q RV G+ GL V DAS+MP++ GNTN+ +MIAE+ A Sbjct: 484 RSDDAMAVVDAQGRVRGVGGLSVADASVMPSITSGNTNSPTVMIAEKVA 532 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: 730 Number of extensions: 32 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: 539 Length adjustment: 35 Effective length of query: 491 Effective length of database: 504 Effective search space: 247464 Effective search space used: 247464 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