Align Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate RR42_RS21615 RR42_RS21615 alcohol dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__Cup4G11:RR42_RS21615 Length = 1000 Score = 218 bits (556), Expect = 6e-61 Identities = 133/391 (34%), Positives = 198/391 (50%), Gaps = 25/391 (6%) Query: 30 SALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPTYGIGRYTFA 89 +A +++G VA GDC CHTA +G AGGL + +P GTIYSTNITPD GIG +++A Sbjct: 601 AATIERGRLVAAAGDCAVCHTAPNGARNAGGLALDTPFGTIYSTNITPDVETGIGNWSYA 660 Query: 90 EFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDKQPDISWP 149 F+ A+R GI +DG LYPA PY +F++ + D+QALYAY M +PV + +++P Sbjct: 661 AFERAMRQGIHRDGRHLYPAFPYTAFAKTSDGDLQALYAYLM-AAEPVRAKAPETALAFP 719 Query: 150 LSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPRGFAMQEKAL 209 ++R + W ++F SPK F P + RG YL G GHC ACH+PR AL Sbjct: 720 YNLRPLMAGWNLLFH-SPKPFEADPARSAQWNRGAYLAEGLGHCSACHSPR------NAL 772 Query: 210 DAAGGPDFLSGGAPIDNWVAPS---LRNDPVVGLGRWSEDDIYTFLKSGRIDHSAVFGGM 266 A G GG + W AP+ L + PV W+E ++++L++G H G Sbjct: 773 GAEQGGRRYLGGGEAEGWEAPALGKLSHAPV----PWTEQALFSYLRTGYAPHHGAAAGP 828 Query: 267 GDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANMLA--SGNTASVPGAD 324 V ++D+ AIA Y+ S P + + + T P A Sbjct: 829 MAPVIEELALLPEEDVRAIAHYVASFGDAQPDAALASAQARQLEQRSADAARTLGGPAAR 888 Query: 325 TYVKECAICHRNDGGGVARMF---PPLAGNPVVVTENPTSLVNVIAHGGVLPPSNWAPSA 381 Y CA+CH++D G R F P LA N + + P +L+ V+ G P+ Sbjct: 889 LYQNACAVCHQSDQG--IRQFGIKPSLALNTNLHGDKPDNLIRVLLDG---IPTPGTSDL 943 Query: 382 VAMPGYSKSLSAQQIADVVNFIRTSWGNKAP 412 MP + +SL +Q+ +V+++R + P Sbjct: 944 GYMPAFGESLDDRQLTQLVHYLRKRFAPDKP 974 Lambda K H 0.317 0.134 0.425 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: 1412 Number of extensions: 82 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: 468 Length of database: 1000 Length adjustment: 39 Effective length of query: 429 Effective length of database: 961 Effective search space: 412269 Effective search space used: 412269 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