Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_019615352.1 G327_RS0113660 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_000381745.1:WP_019615352.1 Length = 561 Score = 427 bits (1098), Expect = e-124 Identities = 232/528 (43%), Positives = 322/528 (60%), Gaps = 10/528 (1%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 ++DY+IVGAGSAGCVLANRLSAD V LLE G D+S I P L+ + T+ W Sbjct: 5 QYDYIIVGAGSAGCVLANRLSADSGNKVLLLETGGSDKSIFIQMPTALSIPMNTKKYAWQ 64 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 F+T +P L R + PRGKVLGGSSSINGM+Y+RGH DF++WQ G + W + LPY Sbjct: 65 FETEAEPFLDNRRMHCPRGKVLGGSSSINGMVYVRGHARDFDEWQQAGAQNWDYAHCLPY 124 Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPAN--RHAASEAFVESALRAGHSYNPDFNGATQEGA 179 F+K+E G ++Y G G L V+ N ++ +AFV + + AG+ D+N QEG Sbjct: 125 FKKAETWSFGGNDYRGESGPLAVNNGNNMKNPLYQAFVNAGVDAGYLATADYNAGQQEGF 184 Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239 G +T+++G RWSTA A+L+P R NLTV+TH V ++L GK A GV KG Sbjct: 185 GPMHMTVKNGVRWSTANAYLRPAMKRDNLTVITHALVHKVLLEGKTAVGVSYESKGQLTE 244 Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299 LR KEV+LSAG+ GSPH+L LSGIG+A L GI HELPGVG+NLQDH + +K Sbjct: 245 LRCNKEVLLSAGSIGSPHILQLSGIGAADTLAQAGIEQVHELPGVGENLQDHLEFYFQFK 304 Query: 300 SNDTSLLGFSLSGGVKMGKAMFDYAR---HRNGPVASNCAEAGAFLKTDPGLERPDIQLH 356 L SL+G + +F R +++G A+N E+ F+++ GLE PD+Q H Sbjct: 305 ----CLKPISLNGKIDPLNKLFIGTRWILNKSGLGATNHFESCGFIRSKAGLEWPDLQYH 360 Query: 357 SVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVAT 416 + + ++ GHGF H+ +PKS G V + S + R AP+I N+L+H DD+ Sbjct: 361 FLPAAMRYDGKEAFAGHGFQVHIGHNKPKSRGRVKVVSSNARTAPQIQFNYLSHQDDIEG 420 Query: 417 LLKGYRITRDIIAQTPMASF-GLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQD 475 R+TR+II Q + + G + D+++ +R ++ YHP +C+MG+D Sbjct: 421 FRACVRLTREIINQPGLDEYRGEEIQPGLAVQTDQEIDSFVRSSVESAYHPSCSCRMGED 480 Query: 476 EMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 M+VV+S+ +VHGIEGLRVVD+SI PT+ GN N+ IM AERAA+ I Sbjct: 481 AMSVVNSETKVHGIEGLRVVDSSIFPTIPNGNLNSPTIMTAERAADII 528 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: 823 Number of extensions: 33 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: 561 Length adjustment: 35 Effective length of query: 491 Effective length of database: 526 Effective search space: 258266 Effective search space used: 258266 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