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_RS23020 BPHYT_RS23020 alcohol dehydrogenase
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__BFirm:BPHYT_RS23020 Length = 451 Score = 460 bits (1183), Expect = e-134 Identities = 225/410 (54%), Positives = 279/410 (68%), Gaps = 2/410 (0%) Query: 17 LAGTALAQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNIT 76 LA A A D+ L+ G Y+AR GDC+ACH+A G+ +AGGL+ +PIG IYSTNIT Sbjct: 28 LAAHAAAPQSRNDTTLIAHGEYLARAGDCIACHSAPSGKPFAGGLKFDTPIGAIYSTNIT 87 Query: 77 PDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKP 136 PD + GIG +TFA+FD AVR G++ +G TLYPAMP+PS++R++++DM ALYAYF HGV P Sbjct: 88 PDRSTGIGSWTFAQFDRAVRAGVKPNGDTLYPAMPFPSYARLSQDDMHALYAYFTHGVAP 147 Query: 137 VAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGAC 196 V Q +K DI WPLSMRWPLGIWR +F+P P F DP IARG YLV G GHCGAC Sbjct: 148 VNQKNKPVDIVWPLSMRWPLGIWRHLFAPEPVSFDAKRYADPVIARGAYLVQGLGHCGAC 207 Query: 197 HTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSGR 256 HTPR MQE+AL GP FL+GGA ID W+ SLR +P G+G WSE D+ FLK+GR Sbjct: 208 HTPRAATMQERALSEFDGPAFLAGGAAIDGWIPSSLRGNPRTGIGAWSEADLVQFLKTGR 267 Query: 257 IDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANMLASGN 316 HSA FGGM DVV S Q+ D DL AIA+YLK+LP P + Y YD + A L G+ Sbjct: 268 TQHSAAFGGMTDVVQHSMQHMNDADLTAIARYLKTLPSTDPQETPYAYDDTAARALRMGD 327 Query: 317 TASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPSN 376 AS PGA Y C CHR+DG G R+FP L GNPVV ++ TSL++V+ G L + Sbjct: 328 -ASAPGAAVYRDNCTACHRSDGRGYNRVFPALGGNPVVQGKDATSLIHVLLTGSTLEGTK 386 Query: 377 WAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLRDT 426 APS+ MP + L+ Q++ADV NF+RTSWGN TV+A DV K+R T Sbjct: 387 TAPSSFTMPAFGWRLNDQEVADVTNFVRTSWGNSG-STVSATDVAKVRKT 435 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: 763 Number of extensions: 46 Number of successful extensions: 3 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: 451 Length adjustment: 33 Effective length of query: 435 Effective length of database: 418 Effective search space: 181830 Effective search space used: 181830 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