Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate BPHYT_RS23020 BPHYT_RS23020 alcohol dehydrogenase
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__BFirm:BPHYT_RS23020 Length = 451 Score = 547 bits (1410), Expect = e-160 Identities = 268/415 (64%), Positives = 313/415 (75%), Gaps = 2/415 (0%) Query: 3 ALVIATLALLGSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPI 62 A V+ L AAA + D L+ GEYLARAGDC+ACH+A GKPFAGGL +TPI Sbjct: 20 AAVLGMTTLAAHAAAPQSRNDT-TLIAHGEYLARAGDCIACHSAPSGKPFAGGLKFDTPI 78 Query: 63 GVIYSTNITPDK-TGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALY 121 G IYSTNITPD+ TGIG ++F FD+AVR GV G TLYPAMPFPSYAR+S DM ALY Sbjct: 79 GAIYSTNITPDRSTGIGSWTFAQFDRAVRAGVKPNGDTLYPAMPFPSYARLSQDDMHALY 138 Query: 122 AYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAYLV 181 AYF GVAPV + N+ DI WPLSMRWPL IWR +FAP + +DPVI+RGAYLV Sbjct: 139 AYFTHGVAPVNQKNKPVDIVWPLSMRWPLGIWRHLFAPEPVSFDAKRYADPVIARGAYLV 198 Query: 182 EGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQ 241 +GLGHCGACHTPRA TMQE+ALS G FL+G A ++GWI SLRG+ + G+G+WSE Sbjct: 199 QGLGHCGACHTPRAATMQERALSEFDGPAFLAGGAAIDGWIPSSLRGNPRTGIGAWSEAD 258 Query: 242 LVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDKQ 301 LVQFLKTGR+ SA FGGM+DVV HSMQ+M DADLTAIARYLK+LP+ DP++ P+ YD Sbjct: 259 LVQFLKTGRTQHSAAFGGMTDVVQHSMQHMNDADLTAIARYLKTLPSTDPQETPYAYDDT 318 Query: 302 VAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVLK 361 A+AL GD S PGAAVY DNC ACHR+DG GY RVFPAL GNPV+Q DATSLIH++L Sbjct: 319 AARALRMGDASAPGAAVYRDNCTACHRSDGRGYNRVFPALGGNPVVQGKDATSLIHVLLT 378 Query: 362 GGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416 G TL T +APS+FTMPAF WRL+DQEVADV NF+R+SWGN S V DVA +R Sbjct: 379 GSTLEGTKTAPSSFTMPAFGWRLNDQEVADVTNFVRTSWGNSGSTVSATDVAKVR 433 Lambda K H 0.316 0.131 0.404 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: 713 Number of extensions: 35 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 434 Length of database: 451 Length adjustment: 32 Effective length of query: 402 Effective length of database: 419 Effective search space: 168438 Effective search space used: 168438 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