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 BPHYT_RS24640 BPHYT_RS24640 alcohol dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__BFirm:BPHYT_RS24640 Length = 426 Score = 391 bits (1005), Expect = e-113 Identities = 212/427 (49%), Positives = 270/427 (63%), Gaps = 11/427 (2%) Query: 1 MINRLKVTFSAAAFSLLAGTALAQTPD--ADSALVQKGAYVARLGDCVACHTALHGQSYA 58 M N LK +A +L AQTP AD ALVQ+GAY+A+ GDCVACHTA G+ +A Sbjct: 1 MKNTLKGFGAALCLTL---PLFAQTPARAADQALVQRGAYLAKAGDCVACHTAPKGKPFA 57 Query: 59 GGLEIKSPIGTIYSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRM 118 GGL + +P+G IY+TNITPDP GIG YT +F A+R G+ KDG LYPAMPYPS++++ Sbjct: 58 GGLPMTTPMGQIYTTNITPDPQTGIGGYTEEDFARAMREGVAKDGHNLYPAMPYPSYAKV 117 Query: 119 TKEDMQALYAYFMHGVKPVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDP 178 +DM+ALYAYFM GV PV Q +++PDI WPL+MRWPL W M+F + PG D Sbjct: 118 NDDDMKALYAYFMSGVAPVQQANREPDIKWPLNMRWPLKFWNMVFLDKGV-YQDKPGKDV 176 Query: 179 EIARGDYLVTGPGHCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVV 238 RG YL+ G GHCG+CHTPRG A QEKALD +G FL+GG +D W A +L + V Sbjct: 177 AWNRGAYLIQGLGHCGSCHTPRGIAFQEKALDESGSA-FLTGGL-LDGWFAANLTGEHNV 234 Query: 239 GLGRWSEDDIYTFLKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPS 298 GLGRW++ D+ FLK+G H++ FG M V+ STQ D D+ A++ YLKSLPP S Sbjct: 235 GLGRWNDQDLQAFLKTGANRHASAFGSMTSVINNSTQGLNDTDIAAMSTYLKSLPPAGGS 294 Query: 299 QG-NYTYDPSTANMLASGNTASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTE 357 Y YDP A ++ A+ GA Y C CH DG G A M PL+GNP V+ + Sbjct: 295 GAPPYKYDPQ-ATKVSLNRPANDAGARVYTAYCMHCHGVDGRGFAPMLAPLSGNPNVLEK 353 Query: 358 NPTSLVNVIAHGGVLPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTA 417 +P+SL+NV +G P+ MP Y+ L+ QQIADV+ F+R W N AP VTA Sbjct: 354 DPSSLINVTLNGTEDLVIGGIPAPYPMPKYAPVLNDQQIADVLTFVRAGWNNGAP-AVTA 412 Query: 418 ADVTKLR 424 DV KLR Sbjct: 413 DDVAKLR 419 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: 727 Number of extensions: 40 Number of successful extensions: 9 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: 426 Length adjustment: 33 Effective length of query: 435 Effective length of database: 393 Effective search space: 170955 Effective search space used: 170955 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: 51 (24.3 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