Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate PfGW456L13_3561 Choline dehydrogenase (EC 1.1.99.1)
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3561 Length = 548 Score = 416 bits (1070), Expect = e-121 Identities = 231/526 (43%), Positives = 314/526 (59%), Gaps = 6/526 (1%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 EFDY++VGAG AGC+LANRLSAD V LLEAG D IH P+G + +W Sbjct: 7 EFDYIVVGAGPAGCLLANRLSADAQHRVLLLEAGGRDNYAWIHIPVGYLFCIGNPRTDWC 66 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 FKT QPGL GR PRGKVLGG SSINGMIY+RG D++ W A GN GW + DVLP Sbjct: 67 FKTEAQPGLQGRALSYPRGKVLGGCSSINGMIYMRGQAGDYDGWAADGNPGWSWRDVLPL 126 Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGAG 180 F++SE H G++E+HG GE V +AF +A ++G + DFN EG G Sbjct: 127 FKQSENHFAGAAEFHGAAGEWRVERQRLSWPILDAFRSAAEQSGIASIDDFNQGDNEGCG 186 Query: 181 YYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHL 240 Y+ V + G RW+ + AFLKP+ R NLTVLT V+ ++L +A+ V A +G Sbjct: 187 YFQVNQKAGIRWNASKAFLKPIGQRPNLTVLTGVEVDRVLLDNGRASAVSARWQGQAKTF 246 Query: 241 RARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKS 300 +ARKE++L AG+ GSP +L SGIG LE GI HEL G G NLQDH + L YK Sbjct: 247 KARKEIVLCAGSVGSPSILQRSGIGPRPLLERLGIGVAHELSGAGGNLQDHLQLRLIYKL 306 Query: 301 NDTSLLGFSLSGGV--KMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSV 358 + L ++G + KMG + Y R+GP++ ++ GAF ++ P +++ H Sbjct: 307 ENARTLN-QIAGSLWGKMGMGL-RYLYDRSGPLSMAPSQLGAFARSGPEQTSANLEYHVQ 364 Query: 359 IGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLL 418 +++ LH F+ VC LRP+S G V + S DP++AP I PN+L+H D+ Sbjct: 365 PLSLERFGEPLHAFPAFTASVCDLRPQSRGRVEIRSADPQEAPLIQPNYLSHPQDLRVAA 424 Query: 419 KGYRITRDIIAQTPMASFG-LRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEM 477 R+TR I+A + +F + + L ++EQL E + TI+HP+GTC+MG D Sbjct: 425 DAIRLTRRIVAAPALRAFNPVEYLPGDSLQSEEQLHEAAARIGTTIFHPVGTCRMGNDAD 484 Query: 478 AVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 AVVD+QL+VHGI GLR+ DASIMP + GNT + +MIAE+AA+ I Sbjct: 485 AVVDAQLKVHGIPGLRIADASIMPRITSGNTCSPTLMIAEKAAQLI 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: 754 Number of extensions: 29 Number of successful extensions: 5 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: 548 Length adjustment: 35 Effective length of query: 491 Effective length of database: 513 Effective search space: 251883 Effective search space used: 251883 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