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 HSERO_RS22810 HSERO_RS22810 alcohol dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__HerbieS:HSERO_RS22810 Length = 423 Score = 342 bits (876), Expect = 2e-98 Identities = 192/426 (45%), Positives = 257/426 (60%), Gaps = 13/426 (3%) Query: 2 INRLKVTFSAAAFSLLAGTALAQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGL 61 + +L F+A A+SL A L AD LV +G Y+AR GDC+ACH+A +Y+GGL Sbjct: 1 MKKLTSLFAALAWSLGALGTLTTAQAADQDLVARGQYLARAGDCMACHSAAGKPAYSGGL 60 Query: 62 EIKSPIGTIYSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKE 121 I S G IYSTNITPD +GIG Y+ A+F AVRHG+R DG+ LYPAMPYPS+++++ E Sbjct: 61 AIDSGHGIIYSTNITPDKEHGIGNYSEAQFSAAVRHGVRADGTQLYPAMPYPSYAKVSDE 120 Query: 122 DMQALYAYFMHGVKPVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIA 181 D+ ALY YFM GV+PVA +S+P ++RW + +W + F+ + K F G EI Sbjct: 121 DIHALYTYFMQGVQPVASTPPASSMSFPFNIRWGMKLWNVFFA-NDKPFREQDGWSAEIK 179 Query: 182 RGDYLVTGPGHCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLG 241 RG YLV G GHCG+CHTPRG AM EKA D++ FLSGG ++ W PSLR G+ Sbjct: 180 RGAYLVEGLGHCGSCHTPRGVAMNEKASDSSQA-QFLSGG-DLNGWAVPSLR-----GMP 232 Query: 242 RWSEDDIYTFLKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGN 301 WS DI +L++GR ++V G M VV ST + +DL A+A YLK+L PV S G+ Sbjct: 233 HWSAQDIVDYLQTGRNKTASVAGEMSLVVEHSTSHLKREDLQAMAAYLKTLSPV-ASSGS 291 Query: 302 YTYDPSTANMLASGNTAS---VPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTEN 358 P + S TA+ G Y+ CA CH G G +FP L G VV EN Sbjct: 292 GRVIPQGVDATVSKLTAAKDLTLGERLYLDNCAACHFVTGRGAPGIFPVLDGATVVNAEN 351 Query: 359 PTSLVNVIAHGGVLPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAA 418 P++L++VI G P + APS + MPG++ LS ++ A + F+R WGN A G V+ Sbjct: 352 PSALLHVILAGARTPSTEKAPSILVMPGFAHRLSDEEAAALATFVRQGWGNHA-GKVSER 410 Query: 419 DVTKLR 424 +V KLR Sbjct: 411 EVGKLR 416 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: 622 Number of extensions: 37 Number of successful extensions: 7 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: 423 Length adjustment: 32 Effective length of query: 436 Effective length of database: 391 Effective search space: 170476 Effective search space used: 170476 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