Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate SM_b20496 SM_b20496 GMC oxidoreductase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Smeli:SM_b20496 Length = 536 Score = 405 bits (1042), Expect = e-117 Identities = 228/530 (43%), Positives = 305/530 (57%), Gaps = 12/530 (2%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 +D++++GAGSAGCVLANRLSADP V LLEAG DR +H P+G + +W Sbjct: 11 YDFIVIGAGSAGCVLANRLSADPKNRVLLLEAGGSDRYHWVHVPIGYLYCMGNPRTDWMM 70 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 +T +PGL GR PRGK+LGG SSINGMIY+RG D++ W+ GN GWG+DDVLPYF Sbjct: 71 RTAAEPGLNGRSLPYPRGKLLGGCSSINGMIYMRGQAADYDGWRQAGNTGWGWDDVLPYF 130 Query: 123 RKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGAGY 181 KSE + G S HG GE V +AF ++A G DFN EG+GY Sbjct: 131 LKSEDNFRGKSPMHGAGGEWRVERQRLSWPILDAFRDAAEELGIPKAEDFNTGDNEGSGY 190 Query: 182 YDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLR 241 ++V R G RW+T+ AFL+P R NL VLT E ++ G++ GV+ + G R Sbjct: 191 FEVNQRGGVRWNTSKAFLRPAMKRPNLRVLTGAETERLIFDGRRTKGVRFRLNGRIQVAR 250 Query: 242 ARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSN 301 A +EVILSAGA SP +L LSG+G + G H+LPGVG+NLQDH + ++ Sbjct: 251 ATREVILSAGAINSPKILELSGVGRPDVVSAAGAEVVHDLPGVGENLQDHLQIRTVFRIE 310 Query: 302 DTSLLG---FSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSV 358 L S+ + MG +Y R+GP++ + G F K+ P + D++ H Sbjct: 311 GAKTLNQLYHSIFSRIGMGA---EYMLRRSGPLSMAPRQLGIFAKSSPSVATADLEYHVQ 367 Query: 359 IGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLL 418 + D LH + VC LRP+S GSV + + + AP I PN+L+ D Sbjct: 368 PLSTDRLGEPLHRYPAVTVSVCNLRPESRGSVHVTTAESSAAPDIRPNYLSTPGDRLLAA 427 Query: 419 KGYRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTD---TIYHPIGTCKMGQD 475 R R+++A +A F +M E EL+R+ D TI+HP+GTCKMG D Sbjct: 428 HAIRHARNLMATKAIARFRPAEMLPGSEFQSED--ELIRRAGDIATTIFHPVGTCKMGTD 485 Query: 476 EMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWIAH 525 MAVVD L+VHG++GLRVVDASIMP++V GNTN+ IMIAE+AAE I H Sbjct: 486 PMAVVDPSLKVHGLDGLRVVDASIMPSIVSGNTNSPVIMIAEKAAEAILH 535 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: 785 Number of extensions: 32 Number of successful extensions: 4 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: 536 Length adjustment: 35 Effective length of query: 491 Effective length of database: 501 Effective search space: 245991 Effective search space used: 245991 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