Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate GFF2991 PGA1_c30400 alcohol dehydrogenase AlkJ
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Phaeo:GFF2991 Length = 529 Score = 376 bits (965), Expect = e-108 Identities = 218/525 (41%), Positives = 298/525 (56%), Gaps = 4/525 (0%) Query: 1 MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNW 60 M +DY+IVGAGSAGCVLANRLSA V LLEAG +D +H P+G + +W Sbjct: 1 MSWDYIIVGAGSAGCVLANRLSA-AGQRVLLLEAGGKDNYHWVHIPMGYLYCINNPRTDW 59 Query: 61 AFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLP 120 ++T + GL GR PRGKVLGG SSINGM+Y+RG D++ W+ G GWG+DDVLP Sbjct: 60 MYRTEAEAGLNGRALIYPRGKVLGGCSSINGMLYLRGQAADYDGWRQRGLTGWGWDDVLP 119 Query: 121 YFRKSEMHHGGSSEYHGGDGELYVSPANRH-AASEAFVESALRAGHSYNPDFNGATQEGA 179 YF+KSE + GSS+ HG GE V H + ++++A G DFN EG Sbjct: 120 YFKKSEDYVDGSSDMHGVGGEWRVENQRLHWDVLDDWMQAAAEWGLPKVTDFNTGNNEGV 179 Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239 GY+ V R G R +TA AFL+ NL V T H I++ +A GV+ G+ Sbjct: 180 GYFRVNQRSGWRMNTAKAFLRTATGE-NLKVETGAHTRRILIENGRAVGVEYSQGGAVKT 238 Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299 R EV+LSAGA SP +L LSG+G A L GIA + ++P VGQNLQDH + ++ Sbjct: 239 ARTGGEVLLSAGAINSPQILQLSGLGPEALLRDHGIAVQRDMPEVGQNLQDHLQLRCAWR 298 Query: 300 SNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVI 359 L + + K +YA R+GP++ ++ GAF ++ P L PD++ H Sbjct: 299 LKGAKTLNTLANSLIGKAKIAAEYAMRRSGPMSMAPSQLGAFSRSRPDLATPDLEYHVQP 358 Query: 360 GTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLK 419 T++ + LH G + VC LRP+S G V + S DP +APRI PN+L+ + D + Sbjct: 359 LTLEAFGQPLHDFPGLTASVCNLRPESRGEVAITSADPMQAPRIAPNYLSTEGDRQVAVA 418 Query: 420 GYRITRDIIAQTPMASFGLRDMYSAGLHND-EQLIELLRKRTDTIYHPIGTCKMGQDEMA 478 R R I+ Q M + +M G ++ L++ TI+HP T +MG +E A Sbjct: 419 AIRQARAIMGQEAMQRYAPVEMKPGGGSDEAADLMQAAGAIGTTIFHPTCTLRMGAEEAA 478 Query: 479 VVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 VD LR+ G+ GLRVVDAS+MP + GNTNA IMIAE+AA+ I Sbjct: 479 PVDGALRLRGVGGLRVVDASVMPVIPSGNTNAPTIMIAEKAADMI 523 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: 770 Number of extensions: 34 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: 529 Length adjustment: 35 Effective length of query: 491 Effective length of database: 494 Effective search space: 242554 Effective search space used: 242554 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