Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate AO353_26740 AO353_26740 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26740 Length = 550 Score = 423 bits (1088), Expect = e-123 Identities = 237/526 (45%), Positives = 317/526 (60%), Gaps = 8/526 (1%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 +DY++VGAG AGC+LANRLSA+P V LLEAG D P IH P+G + +W F Sbjct: 8 YDYIVVGAGPAGCLLANRLSANPQHRVLLLEAGGRDNYPWIHIPVGYLYCIGNPRTDWCF 67 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 KT Q GL GR PRGKVLGGSSSINGMIY+RG D++ W A GN GW ++DVLP F Sbjct: 68 KTEAQTGLQGRSLSYPRGKVLGGSSSINGMIYMRGQAGDYDRWAAEGNPGWSWNDVLPLF 127 Query: 123 RKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGAGY 181 ++SE H G S +HG GE V +AF +A ++G + DFN EG GY Sbjct: 128 KQSENHFAGDSAFHGAAGEWRVERQRLSWPILDAFRSAAEQSGIASVDDFNQGDNEGCGY 187 Query: 182 YDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLR 241 + V + G RW+ A AFLKPVRHR NLTVLT V+ ++L +A+ V A +G Sbjct: 188 FQVNQKAGVRWNAAKAFLKPVRHRPNLTVLTSVDVDRVLLENGRASRVSARWQGQVNIFA 247 Query: 242 ARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSN 301 AR+E+ILSAG+ GSP +L SGIG L+ GI HEL GVG+NLQDH + L YK Sbjct: 248 ARREIILSAGSVGSPSILQRSGIGPGDLLKRLGIGVAHELNGVGRNLQDHLQLRLIYKLE 307 Query: 302 DTSLL---GFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSV 358 + L SL G + MG Y R+GP++ ++ GAF ++ P +++ H Sbjct: 308 NARTLNQIAGSLWGKIGMG---LRYLYDRSGPLSMAPSQLGAFARSGPEQTSANLEYHVQ 364 Query: 359 IGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLL 418 +++ LH F+ VC LRP+S G V + S DP++ P I PN+L+H +D+ Sbjct: 365 PLSLERFGEPLHAFPAFTASVCDLRPQSRGRVEIRSADPQQPPLIQPNYLSHPEDLRVAA 424 Query: 419 KGYRITRDIIAQTPMASFG-LRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEM 477 + R+TR I+A + F + + A L ++EQL E + TI+HP+GTC+MG D Sbjct: 425 EAIRLTRRIVAAPALQPFNPVEYLPGAALQSEEQLHEAAARIGTTIFHPVGTCRMGNDAD 484 Query: 478 AVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 AVVD+QLRVHGI GLR+ DASIMP + GNT + +MIAE+AA+ I Sbjct: 485 AVVDAQLRVHGIPGLRIADASIMPHITSGNTCSPTLMIAEKAAQLI 530 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: 760 Number of extensions: 32 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: 550 Length adjustment: 35 Effective length of query: 491 Effective length of database: 515 Effective search space: 252865 Effective search space used: 252865 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