Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_054343390.1 Nant_RS19700 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_001305295.1:WP_054343390.1 Length = 579 Score = 381 bits (979), Expect = e-110 Identities = 221/542 (40%), Positives = 313/542 (57%), Gaps = 22/542 (4%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 +DY+IVGAGSAGCVLANRL+ D TV LLEAG D+S I P L+ + T W F Sbjct: 7 YDYIIVGAGSAGCVLANRLTEDGQHTVLLLEAGGSDKSIFIQMPTALSYPMNTPKYAWQF 66 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 T +P L GR + PRGKVLGGSSSINGM+Y+RGH DF++W G GWG+ LPYF Sbjct: 67 HTEGEPFLDGRSMHCPRGKVLGGSSSINGMVYVRGHACDFDEWSEKGATGWGYQQCLPYF 126 Query: 123 RKSEMHHGGSSEYHGGDGELYVSPAN---RHAASEAFVESALRAGHSYNPDFNGATQEGA 179 +K+E GS +Y GG G L+ N + +AF+++ AG+ D+NG QEG Sbjct: 127 KKAETWAKGSDDYRGGSGPLFTCNGNDMKLNPLYQAFIDAGEDAGYPTTDDYNGYRQEGF 186 Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQ--------- 230 G +T++ G R ST+ A+L+ R NLT+++ +++ GK+A G++ Sbjct: 187 GAMHMTVKAGVRASTSNAYLRDAMQRPNLTLISGVLTRKVIMEGKRAVGIEYEKMDSEKK 246 Query: 231 -----ALIKGSRV-HLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGV 284 + K +RV + A KEVIL+AG+ GSPHLL LSGIG A LE G+A H+LPGV Sbjct: 247 SSEKKSSDKSARVINATANKEVILAAGSIGSPHLLQLSGIGPAKVLEEAGVALVHDLPGV 306 Query: 285 GQNLQDHADVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKT 344 G+NLQDH ++ Y L L V G + ++G A+N E+ F+++ Sbjct: 307 GENLQDHLEIYFQYHCKQPITLNGKLD-LVSKGLIGARWMLFKDGLGATNHFESCGFIRS 365 Query: 345 DPGLERPDIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRID 404 GL+ P+IQ H + + K GHGF HV +P+S G V + S DP+ P I Sbjct: 366 RKGLKWPNIQYHFLPAAMRYDGGKAIEGHGFQVHVGPNKPQSRGRVWIKSADPKAKPSIV 425 Query: 405 PNFLAHDDDVATLLKGYRITRDIIAQTPMASF-GLRDMYSAGLHNDEQLIELLRKRTDTI 463 N++ + D R+TR+I+ Q + ++ G A + +D + +R+ ++ Sbjct: 426 FNYIGTEQDKQDWRDCIRLTREILKQPALDAYRGDEVQPGAQVSSDIDVDRWVRENVESA 485 Query: 464 YHPIGTCKMGQDE--MAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521 YHP TCK+G D+ MAV+D+Q RV G+E LRVVD+S+ PT+ GN NA IM+AE+AA+ Sbjct: 486 YHPSCTCKIGADDDAMAVLDTQCRVRGVESLRVVDSSVFPTIPNGNLNAPTIMVAEKAAD 545 Query: 522 WI 523 I Sbjct: 546 MI 547 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: 832 Number of extensions: 47 Number of successful extensions: 6 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: 579 Length adjustment: 36 Effective length of query: 490 Effective length of database: 543 Effective search space: 266070 Effective search space used: 266070 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: 53 (25.0 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