Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate BPHYT_RS23020 BPHYT_RS23020 alcohol dehydrogenase
Query= BRENDA::C7G3B8 (472 letters) >FitnessBrowser__BFirm:BPHYT_RS23020 Length = 451 Score = 456 bits (1174), Expect = e-133 Identities = 232/444 (52%), Positives = 288/444 (64%), Gaps = 11/444 (2%) Query: 3 INRLKAALGAVAVGLLAG--TSLAHA----QNADEDLIKKGEYVARLGDCVACHTSLNGQ 56 I RL A+ V + G T AHA D LI GEY+AR GDC+ACH++ +G+ Sbjct: 7 IQRLTQAMKRVGAAAVLGMTTLAAHAAAPQSRNDTTLIAHGEYLARAGDCIACHSAPSGK 66 Query: 57 KYAGGLSIKTPIGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSF 116 +AGGL TPIG IYSTNITPD + GIG++TF +FD AVR GV+ +G TLYPAMP+PS+ Sbjct: 67 PFAGGLKFDTPIGAIYSTNITPDRSTGIGSWTFAQFDRAVRAGVKPNGDTLYPAMPFPSY 126 Query: 117 ARMTQDDMKALYAYFMHGAQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPG 176 AR++QDDM ALYAYF HG P+ QKN P DI WP+SMRWPL IWR +FAP P F Sbjct: 127 ARLSQDDMHALYAYFTHGVAPVNQKNKPVDIVWPLSMRWPLGIWRHLFAPEPVSFDAKRY 186 Query: 177 TDAEIARGEYLVTGPGHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRND 236 D IARG YLV G GHCGACHTPR MQE+AL GP FL GG ID WI SLR + Sbjct: 187 ADPVIARGAYLVQGLGHCGACHTPRAATMQERALSEFDGPAFLAGGAAIDGWIPSSLRGN 246 Query: 237 PVLGLGRWSDEDLFLFLKSGRTDHSAAFGGMADVVGWSTQYFTDADLHAMVKYIKSLPPV 296 P G+G WS+ DL FLK+GRT HSAAFGGM DVV S Q+ DADL A+ +Y+K+LP Sbjct: 247 PRTGIGAWSEADLVQFLKTGRTQHSAAFGGMTDVVQHSMQHMNDADLTAIARYLKTLPST 306 Query: 297 PPARGDYSYDASTAQMLDSNNISGNAGAKTYVDQCAICHRNDGGGVARMFPPLAGNPVVV 356 P Y+YD + A+ L + S GA Y D C CHR+DG G R+FP L GNPVV Sbjct: 307 DPQETPYAYDDTAARALRMGDASA-PGAAVYRDNCTACHRSDGRGYNRVFPALGGNPVVQ 365 Query: 357 SDNPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANT 416 + TS+ H+++ G L T APS+ MP + L+DQ++ADV NF+R++WGN + + Sbjct: 366 GKDATSLIHVLLTGSTLEGTKTAPSSFTMPAFGWRLNDQEVADVTNFVRTSWGN-SGSTV 424 Query: 417 TAADIQKLRLD---HTPLPTPGWA 437 +A D+ K+R H P PG A Sbjct: 425 SATDVAKVRKTVTVHAPDMPPGAA 448 Lambda K H 0.318 0.135 0.430 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: 35 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: 472 Length of database: 451 Length adjustment: 33 Effective length of query: 439 Effective length of database: 418 Effective search space: 183502 Effective search space used: 183502 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 (21.7 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