Align quinoprotein decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate RR42_RS05285 RR42_RS05285 quinonprotein alcohol dehydrogenase
Query= CharProtDB::CH_107432 (595 letters) >FitnessBrowser__Cup4G11:RR42_RS05285 Length = 582 Score = 307 bits (786), Expect = 9e-88 Identities = 189/518 (36%), Positives = 279/518 (53%), Gaps = 36/518 (6%) Query: 46 TNGLGVQGQRYSPLDLLNANNVKELRPVWAFSFGGEKQRGQQAQPLIKDGVMYLTGSYSR 105 +NG VQ RY P +N NV +L+P AF F + P++ +GVM+LT SY+ Sbjct: 72 SNGSYVQ-TRYYPGSQINTRNVAKLKP--AFLFQTAVLESMETAPIVVNGVMFLTTSYNH 128 Query: 106 VFAVDARTGKKLWQYDARLPDDIRPCCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKV 165 V+A+DA TGK+ W Y ++ CC NRGVA+ GD VF GTLDA+LVAL+ TGK+ Sbjct: 129 VYAIDAVTGKEFWHYKHKMGPITTFCCGPNNRGVAVSGDRVFMGTLDARLVALDARTGKL 188 Query: 166 VWSKKVADHKEGYSISAAPMIVNGKLITGVAGGEFGVVGKIQAYNPENGELLWMRPTV-- 223 +W ++AD + GYS + AP++V+ K++ G GGE+G+ G ++AY+ +G+LLW T+ Sbjct: 189 LWETQIADPELGYSETMAPVVVDDKILIGTNGGEYGIRGFLKAYSATDGKLLWTFYTIPE 248 Query: 224 EGHMG-YVYKD--GKAIENGISGGE---AGKTWPGDLWKTGGAAPWLGGYYDPETNLILF 277 +GH G + +D G+ ++ I+ + A K GD +K G W+ D + + +F Sbjct: 249 KGHEGVWATRDATGRDMKRDIAAEKKQLADK--GGDFYKALGGGVWMPPAIDRKNRMAIF 306 Query: 278 GTGNPAP-WNSHLRPGDNLYSSSRLALNPDDGTIKWHFQSTPHDGWDFDGVNELISFNYK 336 GNP+P +RPGDNLY+ S +A++ D G KWH Q HD WD D V+ I + + Sbjct: 307 VVGNPSPDLYGAIRPGDNLYTDSMVAVDLDTGAYKWHSQYIAHDVWDLDAVSPPILVDVR 366 Query: 337 D-GGKEVKAAATADRNGFFYVLDRTNGKFIRGFPFVDKITWATGLDKDGRPIYNDASRPG 395 D G+ + + G YV DR +G+ IR + P + + P Sbjct: 367 DKNGQMIPGVIHGGKTGHVYVHDRRDGRLIR-------------FSQAMIPQEDMWTLPT 413 Query: 396 APGSEAKGSSVFVAPAFLGAKNWMPMAYNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFL 455 A G+ + P G W PMA+N T + Y + M E Y G +L Sbjct: 414 ANGAR-------MLPGANGGVEWSPMAFNPKTRMAYAANLHQPMTYQVEASPYPGGKLWL 466 Query: 456 GAGFTIKPLNEDYIGVLRAIDPISGKEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQA 515 G F P + G L A++ +GK VW +K PL GGVL T G LVF G G +A Sbjct: 467 GGAFKTIPAEAQW-GKLSAVNIDTGKVVWDYKTDQPLIGGVLATAGGLVFNGEGNGLFRA 525 Query: 516 FNAKTGDKVWEFQTGSGVLGSPVTWEMDGEQYVSVVSG 553 F+A TG K+WE+Q G+GV V++ + G+QY++V +G Sbjct: 526 FDAATGKKLWEYQCGAGVNAPAVSYMVGGKQYIAVAAG 563 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: 1316 Number of extensions: 96 Number of successful extensions: 17 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: 595 Length of database: 582 Length adjustment: 37 Effective length of query: 558 Effective length of database: 545 Effective search space: 304110 Effective search space used: 304110 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