Align Alcohol dehydrogenase (quinone), dehydrogenase subunit; ADH; Alcohol dehydrogenase (quinone), acceptor subunit; Alcohol dehydrogenase (quinone), subunit I; Ethanol:Q2 reductase; G3-ADH subunit I; Quinohemoprotein alcohol dehydrogenase; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate RR42_RS05285 RR42_RS05285 quinonprotein alcohol dehydrogenase
Query= SwissProt::O05542 (757 letters) >FitnessBrowser__Cup4G11:RR42_RS05285 Length = 582 Score = 273 bits (699), Expect = 1e-77 Identities = 200/596 (33%), Positives = 282/596 (47%), Gaps = 73/596 (12%) Query: 16 LLSCAAALAFSAAVPVAFAQEDT-------GTAITSS---------DNGGHPG-DWLSYG 58 LL A A A +A +P AF ++ G A+T D G+ DW+ Sbjct: 14 LLLLALAAAAAALIPAAFGADEIQGGATTPGAAMTRPLPPVTQAQLDAAGNDARDWVHSN 73 Query: 59 RSYSEQRYSPLDQINTENVGKLKLAWHYDLDTNRGQEGTPLIVNGVMYATTNWSKMKALD 118 SY + RY P QINT NV KLK A+ + E P++VNGVM+ TT+++ + A+D Sbjct: 74 GSYVQTRYYPGSQINTRNVAKLKPAFLFQTAVLESMETAPIVVNGVMFLTTSYNHVYAID 133 Query: 119 AATGKLLWSYDPKVPGNIADRGCCDTVSRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWS 178 A TGK W Y K+ G I CC +RG A +V+ GT D RL+ALDA+TGKL+W Sbjct: 134 AVTGKEFWHYKHKM-GPIT-TFCCGPNNRGVAVSGDRVFMGTLDARLVALDARTGKLLWE 191 Query: 179 VYTIPKEAQLGHQRSYTVDGAPRIAKGKVLIGNGGAEFGARGFVSAFDAETGKLDWRFFT 238 T + +LG Y+ AP + K+LIG G E+G RGF+ A+ A GKL W F+T Sbjct: 192 --TQIADPELG----YSETMAPVVVDDKILIGTNGGEYGIRGFLKAYSATDGKLLWTFYT 245 Query: 239 VPNPENKPDGAASD--------DILMSKAYPTWGKNGAWKQQGGGGTVWDSLVYDPVTDL 290 +P ++ A D DI K +K GGG VW D + Sbjct: 246 IPEKGHEGVWATRDATGRDMKRDIAAEKKQLADKGGDFYKALGGG--VWMPPAIDRKNRM 303 Query: 291 VYLGVGNGSPWNYKFRSEGKGDNLFLGSIVAINPDTGKYVWHFQETPMDEWDYTSVQQIM 350 VGN SP Y + GDNL+ S+VA++ DTG Y WH Q D WD +V + Sbjct: 304 AIFVVGNPSPDLY--GAIRPGDNLYTDSMVAVDLDTGAYKWHSQYIAHDVWDLDAVSPPI 361 Query: 351 TLDM-PVNGEMRHVIVHAPKNGFFYIIDAKTGKFITGKPYTYENWANGLDPVTGRPNYVP 409 +D+ NG+M ++H K G Y+ D + G+ I ++ + P Sbjct: 362 LVDVRDKNGQMIPGVIHGGKTGHVYVHDRRDGRLI--------RFSQAMIP--------Q 405 Query: 410 DALWTL-TGKPWLGIPGELGGHNFAAMAYSPKTKLVYIPAQQIPLLYDGQKGGFKAYHDA 468 + +WTL T +PG GG ++ MA++PKT++ Y P+ Y + + Sbjct: 406 EDMWTLPTANGARMLPGANGGVEWSPMAFNPKTRMAYAANLHQPMTYQVEASPYPG-GKL 464 Query: 469 WNLGLDMNKIGLFDDNDPEHVAAKKDFLKVLKGWTVAWDPEKMAPAFTINHKGPWNGGLL 528 W LG G F E K + + G V WD + P GG+L Sbjct: 465 W-LG------GAFKTIPAEAQWGKLSAVNIDTG-KVVWDYKTDQPLI---------GGVL 507 Query: 529 ATAGNVIFQGLANGEFHAYDATNGNDLYSFPAQSAIIAPPVTYTANGKQYVAVEVG 584 ATAG ++F G NG F A+DA G L+ + + + AP V+Y GKQY+AV G Sbjct: 508 ATAGGLVFNGEGNGLFRAFDAATGKKLWEYQCGAGVNAPAVSYMVGGKQYIAVAAG 563 Lambda K H 0.317 0.136 0.435 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: 1550 Number of extensions: 122 Number of successful extensions: 22 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: 757 Length of database: 582 Length adjustment: 38 Effective length of query: 719 Effective length of database: 544 Effective search space: 391136 Effective search space used: 391136 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: 54 (25.4 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