Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_028741798.1 RL_RS31805 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_000009265.1:WP_028741798.1 Length = 531 Score = 407 bits (1045), Expect = e-118 Identities = 223/523 (42%), Positives = 301/523 (57%), Gaps = 2/523 (0%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 +DY+I+GAGSAGCVLANRLSAD V LLEAG D IH P+G + +W F Sbjct: 4 YDYIIIGAGSAGCVLANRLSADGRSRVLLLEAGGSDNYHWIHIPVGYLYCINNPRTDWCF 63 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 T P+ GL GR PRGKVLGG SSINGMIY+RG D++ W+ +G GWG+DD+LP+F Sbjct: 64 TTAPEAGLNGRALSYPRGKVLGGCSSINGMIYMRGQARDYDLWRQMGCSGWGWDDILPFF 123 Query: 123 RKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGAGY 181 RKSE + G E HG GE + A R A +AF ++A AG DFN + EG+GY Sbjct: 124 RKSEDFYRGEDEMHGAGGEWRIEKARVRWAVLDAFQQAAREAGIPETADFNRGSNEGSGY 183 Query: 182 YDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLR 241 +DV R G RW+T+ AFL+P RSNLTVLT V +++ GV+ +G Sbjct: 184 FDVNQRSGIRWNTSKAFLRPAMRRSNLTVLTKAQVRRLLVEEGAVAGVEFQHRGVAKRAY 243 Query: 242 ARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSN 301 A KE +LSAG+ GSPH+L LSGIG L+ G+ E+ GVG+NLQDH + L YK Sbjct: 244 AAKETVLSAGSIGSPHILELSGIGRGEVLQRAGVDVVTEVKGVGENLQDHLQLRLAYKVT 303 Query: 302 DTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIGT 361 L + + +Y R+GP+A ++ G F ++ P E PD+Q H + Sbjct: 304 GVPTLNEKATKLIGKAAIGLEYLVRRSGPMAMAPSQLGIFTRSGPDRETPDLQYHVQPVS 363 Query: 362 VDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLKGY 421 ++ +H + VC LRP+S GSV L+SPD P I P +L+ D ++ Sbjct: 364 LEKFGDPVHPFPAITASVCNLRPESRGSVHLSSPDFAAQPTISPKYLSTQRDRDIAVRSI 423 Query: 422 RITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRT-DTIYHPIGTCKMGQDEMAVV 480 R+TR I+AQ A F + + E +E TI+HP+GTC+MG D +VV Sbjct: 424 RLTRKIVAQPSFACFRPEEFKPGPAYQTEADLERAAGEIGTTIFHPVGTCRMGADRDSVV 483 Query: 481 DSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 D +LR+ + LR+ DAS+MP++ GNTN+ IMIAE+AA I Sbjct: 484 DPRLRLRALGKLRIADASVMPSITSGNTNSPTIMIAEKAAAMI 526 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: 717 Number of extensions: 35 Number of successful extensions: 3 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: 531 Length adjustment: 35 Effective length of query: 491 Effective length of database: 496 Effective search space: 243536 Effective search space used: 243536 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 24 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