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_RS01060 BPHYT_RS01060 alcohol dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__BFirm:BPHYT_RS01060 Length = 417 Score = 408 bits (1049), Expect = e-118 Identities = 213/415 (51%), Positives = 276/415 (66%), Gaps = 21/415 (5%) Query: 29 DSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPTYGIGRYTF 88 D+AL+++GAY+A LGDC ACH A G+++ GGL I +PIGT+Y+TNITPDP GIG YT Sbjct: 4 DTALIRRGAYLAVLGDCAACHVAKDGKAFVGGLPITTPIGTLYTTNITPDPATGIGNYTP 63 Query: 89 AEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDKQPDISW 148 ++F+ AVR GIR+DGS +YPAMPYPS++ ++ +D++ALYAYFMHGV PV P++ I W Sbjct: 64 SDFERAVRRGIRRDGSPMYPAMPYPSYAHVSDDDVRALYAYFMHGVAPVDSPNRASGIPW 123 Query: 149 PLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIA-------------RGDYLVTGPGHCGA 195 PLSMRWPL WR F+P + PA TD + A RG YLV G HCG+ Sbjct: 124 PLSMRWPLTYWRWAFAPKVQ---PAAHTDIDSATAAGAAHDAALLERGRYLVEGLMHCGS 180 Query: 196 CHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSG 255 CHTPRG +QEKAL A G D+LSGG ID++VA SLR D + GLGRWS+ DI FL++G Sbjct: 181 CHTPRGVGLQEKALGDADGSDYLSGGV-IDHYVANSLRGDDLTGLGRWSQADIVEFLRTG 239 Query: 256 RIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANMLASG 315 R +A FGGM DVV S+Q+ D DL A+A YLKSLP P+ G+Y Y + LA G Sbjct: 240 RNPETAAFGGMRDVVQHSSQFLNDTDLLAVATYLKSLPGNHPA-GHYAYAAAAGAALAKG 298 Query: 316 NTASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPS 375 + S GA Y+ CA CH + G G FP LAGNPVV ++PTSL+N++ +G + Sbjct: 299 D-VSARGAIDYLNSCAACHLSSGKGYRDTFPALAGNPVVNAKDPTSLINIVLNGNTEVGT 357 Query: 376 NWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLR-DTGAP 429 + P+ MP + L+ ++A+VV FIRTSWGN AP V A +V K+R T AP Sbjct: 358 SRVPTQFTMPPFGDRLTDAEVANVVTFIRTSWGNHAP-DVNADEVAKVRAQTHAP 411 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: 722 Number of extensions: 33 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: 417 Length adjustment: 32 Effective length of query: 436 Effective length of database: 385 Effective search space: 167860 Effective search space used: 167860 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