Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_043526943.1 JH15_RS03245 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_000759345.1:WP_043526943.1 Length = 563 Score = 363 bits (931), Expect = e-104 Identities = 213/527 (40%), Positives = 300/527 (56%), Gaps = 8/527 (1%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHT--PLGLAAILPTRHVN 59 E+DY+I+GAGSAG VLA RL+ D V+V LLEAG D T P LA L + N Sbjct: 6 EYDYIIIGAGSAGNVLATRLTEDADVSVLLLEAGGPDYRFDFRTQMPAALAYPLQGKRYN 65 Query: 60 WAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDW-QALGNEGWGFDDV 118 WAF+T P+P + R RGK LGGSS INGM Y+RG+ D++ W + G E W + + Sbjct: 66 WAFETDPEPYMNDRRMECGRGKGLGGSSLINGMCYLRGNALDYDSWAKQPGLEDWNYLEC 125 Query: 119 LPYFRKSEMHHGGSSEYHGGDGELYVSPANR--HAASEAFVESALRAGHSYNPDFNGATQ 176 LPYF+++E G + YHGG+G + V+ + AF+++ + AG+ D NG Q Sbjct: 126 LPYFKRAETRDIGPNTYHGGEGPVSVATPKEGNNELYGAFIQAGIEAGYPATEDVNGYQQ 185 Query: 177 EGAGYYD-VTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKG 235 EG G D T +GRR STA +L + R NLT+ TH + I+ GK+A GV KG Sbjct: 186 EGFGPMDRTTTPNGRRASTARGYLDVAKRRDNLTIETHAVTDRILFEGKRAVGVAYARKG 245 Query: 236 SRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVV 295 + +RAR+EV+L GA SP +L+ SG+G+A L+ I H+LPGVG+NLQDH ++ Sbjct: 246 AAQEVRARREVLLCGGAIASPQILLRSGVGNAEHLKEYDIPVVHDLPGVGENLQDHLEMY 305 Query: 296 LCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQL 355 + Y+ + + K ++ G +SN EA F++T+ P++Q Sbjct: 306 IQYECT-KPISFYPALKWYNQPKIGAEWLFFGTGIGSSNQFEAAGFIRTNDDEAWPNLQY 364 Query: 356 HSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVA 415 H + + + + HGF HV +R S G + L S DP AP I N+++ D Sbjct: 365 HFLPIAISYNGKSAVQAHGFQAHVGSMRSMSRGRIRLTSKDPNAAPSILFNYMSEQKDWE 424 Query: 416 TLLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQ 474 R+TR+IIAQ M + R++ + DE+L E +R+ +T YHP G+CKMG Sbjct: 425 EFRDAIRLTREIIAQPAMDPYRGREISPGPNVQTDEELDEFVRQHAETAYHPSGSCKMGY 484 Query: 475 DEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521 D+MAVVD RVHG+E LRV+DASIMP + GN NA IMIAE+ A+ Sbjct: 485 DDMAVVDGAGRVHGLENLRVIDASIMPVITTGNLNAPTIMIAEKMAD 531 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: 876 Number of extensions: 45 Number of successful extensions: 7 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: 563 Length adjustment: 35 Effective length of query: 491 Effective length of database: 528 Effective search space: 259248 Effective search space used: 259248 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