Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate 3610403 Dshi_3784 Gluconate 2-dehydrogenase (acceptor) (RefSeq)
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__Dino:3610403 Length = 305 Score = 165 bits (417), Expect = 2e-45 Identities = 103/264 (39%), Positives = 143/264 (54%), Gaps = 20/264 (7%) Query: 28 VQQGEYLARAGDCVACHTAKD--GKPFAGGLPMETPIGVIYSTNITPD-KTGIGDYSFED 84 V +G YLARA C+ACHT + G P AGG P+ETP G Y N+T D + G+G+++ E Sbjct: 40 VDRGAYLARASGCIACHTNFEAGGAPLAGGAPLETPFGTFYPPNLTTDPEHGMGEWTAEQ 99 Query: 85 FDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGVAPVARDNQDSDIPWPL 144 F KAVR G+ G+ YP+ P+ YA SD D+ L+A F + V PV ++D+ +P Sbjct: 100 FAKAVRQGIGPDGTPYYPSFPYTFYADFSDQDIADLWAAF-QTVPPVDEPAPENDVSFPF 158 Query: 145 SMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAYLVEGLGHCGACHTPRALTMQEKALS 204 RW L +WR F +T P G +RG LV G HCGACHTPR L Sbjct: 159 DQRWGLKLWRAAFFYDPDT-EPIEGRSDAWNRGRELVRGAAHCGACHTPRNL-------- 209 Query: 205 ASGGSDF---LSGSAPLEGWIAKSLRGDHKDGL-GSWSEEQLVQFLKTGRSDRSAVFGG- 259 +GG D +G+A L G +K+ KD + W+ L L+TG + FGG Sbjct: 210 -AGGRDIGASFAGNAQLPGG-SKAPAIRPKDLVKNDWTVSNLAYALQTGITPSGDAFGGS 267 Query: 260 MSDVVVHSMQYMTDADLTAIARYL 283 M++VV +++T AD A+A +L Sbjct: 268 MAEVVREGTRFLTPADREAMALFL 291 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: 457 Number of extensions: 40 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: 434 Length of database: 305 Length adjustment: 29 Effective length of query: 405 Effective length of database: 276 Effective search space: 111780 Effective search space used: 111780 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: 49 (23.5 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