Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate CCNA_01337 CCNA_01337 GMC family oxidoreductase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Caulo:CCNA_01337 Length = 540 Score = 395 bits (1015), Expect = e-114 Identities = 219/527 (41%), Positives = 303/527 (57%), Gaps = 6/527 (1%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 ++DY++VGAGSAGC+LANRLSADP V LLEAG +D H P+G + +W Sbjct: 10 DYDYIVVGAGSAGCLLANRLSADPRRRVLLLEAGGDDNWIWFHVPVGYLFAIGNPRADWM 69 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 +TTPQ GL GRV PRGKV+GGSS+IN MIY+RG D++ W+ G GWG+ DVLPY Sbjct: 70 LETTPQAGLDGRVLAYPRGKVIGGSSAINAMIYMRGQARDYDGWRQRGLAGWGWPDVLPY 129 Query: 122 FRKSEMHHGGSSEYHGGDGELYVS-PANRHAASEAFVESALRAGHSYNPDFNGATQEGAG 180 F K E H E+H GE V P R +A + +AG + DFNG G+ Sbjct: 130 FLKHEDHIDPRGEHHRAGGEYRVEHPRVRWDVLDAIRRAGEQAGIAQVDDFNGGDNAGSS 189 Query: 181 YYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHL 240 Y+ V R GRRWSTATAFLKPV R NL ++ VE +++ GK+ G++ G+ V Sbjct: 190 YFQVNQRAGRRWSTATAFLKPVLSRPNLRLVKGVEVERLIIDGKRVRGLRGRRGGAAVTA 249 Query: 241 RARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKS 300 E+IL+AGA GSP +L SGIG L G+A H+LPGVG NLQDH + +K Sbjct: 250 SVSGELILAAGAIGSPVILQRSGIGRGETLSRAGVAMVHDLPGVGANLQDHLQIRPVFKV 309 Query: 301 NDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIG 360 + L + + DY R+GP+ ++ G F ++ P E +++ H Sbjct: 310 SGVRTLNTDYANLFRRAGMGLDYLLRRSGPLTMAPSQLGMFCRSGPEYESANLEFHFQPL 369 Query: 361 TVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLKG 420 ++D LH + VC LRP S G+V L+ P +PRIDPN+LA ++D ++ Sbjct: 370 SLDRWGEGLHRFGAVTASVCNLRPSSRGAVSLSGPGLEHSPRIDPNYLATEEDRRVAVES 429 Query: 421 YRITRDIIAQTPMASFGLRDMYSAG--LHNDEQLIELLRKRTDTIYHPIGTCKMGQ--DE 476 + R I+ Q +A++ + + G + D L+ + TI+HP+GT MG D Sbjct: 430 LKWARRIMGQAALAAYA-PEAFRPGPEVDGDAALLAAAKALATTIFHPVGTAAMGADGDP 488 Query: 477 MAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 +AV+D++LRV G+EGLRV+DAS MPT+ GNTNA +MIAE+ A I Sbjct: 489 LAVLDARLRVRGVEGLRVIDASAMPTITSGNTNAPTVMIAEKGAAMI 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: 828 Number of extensions: 49 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: 540 Length adjustment: 35 Effective length of query: 491 Effective length of database: 505 Effective search space: 247955 Effective search space used: 247955 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