Align quinoprotein decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate H281DRAFT_00328 H281DRAFT_00328 alcohol dehydrogenase (cytochrome c)
Query= CharProtDB::CH_107432 (595 letters) >FitnessBrowser__Burk376:H281DRAFT_00328 Length = 575 Score = 420 bits (1080), Expect = e-122 Identities = 214/535 (40%), Positives = 317/535 (59%), Gaps = 27/535 (5%) Query: 53 GQRYSPLDLLNANNVKELRPVWAFSFGGEKQRGQQAQPLIKDGVMYLTGSYSRVFAVDAR 112 GQ +SPL ++ +NVK+L+ VW++ F + Q+G +A P++ +++T V+A DA Sbjct: 61 GQAHSPLKQIDTSNVKQLKQVWSYKFPADLQQGFEATPIVNGHYLFVTTPKDNVYAFDAA 120 Query: 113 TGKKLWQYDARLPDDI--RPCCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKK 170 +GK+LW+++ +L + CCDVINRGVALYG V+ L+ ++VAL+ TG + W K Sbjct: 121 SGKQLWKFEPKLGAESFKTACCDVINRGVALYGKNVYVAMLNGEVVALDAQTGSLAWRKT 180 Query: 171 VADHKEGYSISAAPMIVNGKLITGVAGGEFGVVGKIQAYNPENGELLWMRPTVEGHMGYV 230 + + GY+ S AP+ ++G L+ G AGGE+G G I A NP+NG +LW R TV Sbjct: 181 MFEPGVGYAFSLAPLAIDGALVVGSAGGEYGARGFIAALNPDNGNVLWKRFTVPA----- 235 Query: 231 YKDGKAIENGISGGEAGKTWPGDLWKTGGAAPWLGGYYDPETNLILFGTGNPAPWNSHLR 290 +G + TWP + + GGA WL G YD + + +G GNP PW + LR Sbjct: 236 -----------AGEKGANTWPDGMQEHGGAPAWLTGTYDAASRTLYWGVGNPGPWLADLR 284 Query: 291 PGDNLYSSSRLALNPDDGTIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEVKAAATADR 350 PGDNLYS S LAL+P G +KWH+Q T HD WD+DGVN + N K K A ADR Sbjct: 285 PGDNLYSDSLLALDPKTGDLKWHYQYTKHDTWDYDGVNTPVLANIKYQDKNYDAIIHADR 344 Query: 351 NGFFYVLDRTNGKFIRGFPFVDKITWATGLDKDGRPIYNDASRPGAPGSEAKGSSVFVAP 410 NG+F+ +DR GK I PFV K T TG DG P+ + + P G+++ P Sbjct: 345 NGYFHAIDRGTGKLIYAKPFV-KATSVTGYTADGVPVQDPSKYP------KTGTTIETCP 397 Query: 411 AFLGAKNWMPMAYNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKP-LNEDYI 469 +FLG KNW ++Y+ D + VP+ M + + + Y +G +LG GF IKP Sbjct: 398 SFLGGKNWWSVSYDPDRQVAIVPALHACMSLSGKSVTYMEGLPYLGEGFEIKPEPGSKGY 457 Query: 470 GVLRAIDPISGKEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGDKVWEF-Q 528 G L+AID +GK++W + + P GGV TT L F+G+ +G L AF++ TG +W+ + Sbjct: 458 GELQAIDVTTGKKMWSYWSKLPWNGGVATTASGLAFSGSLDGHLYAFDSSTGKVLWKSPK 517 Query: 529 TGSGVLGSPVTWEMDGEQYVSVVSGWGGAVPLWGGEVAKRVKDFNQGGMLWTFKL 583 SG++ P +E+DG++YV++++G+GGA P+WGG +AK + +GG L+ F L Sbjct: 518 LASGIVAQPSVFEVDGKEYVAILAGYGGANPIWGGPMAKAAEKIPRGGTLYVFAL 572 Lambda K H 0.317 0.137 0.438 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: 1413 Number of extensions: 117 Number of successful extensions: 18 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 595 Length of database: 575 Length adjustment: 37 Effective length of query: 558 Effective length of database: 538 Effective search space: 300204 Effective search space used: 300204 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 53 (25.0 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