Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate GFF2578 PS417_13140 oxidoreductase
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__WCS417:GFF2578 Length = 385 Score = 192 bits (488), Expect = 1e-53 Identities = 132/345 (38%), Positives = 187/345 (54%), Gaps = 44/345 (12%) Query: 26 VVGGLEVPWALAFLPDG-GMLIAERPGRIRLFR-EGRLSTYAE-LP-VYHRGESGLLGLA 81 + GL+ PWA+AFLPD G L+ ERPG +R +G+LS + +P V+ +G+ GLL + Sbjct: 42 IAKGLDHPWAVAFLPDKQGFLVTERPGHLRFVSPDGKLSAPLKGVPEVWAKGQGGLLDVV 101 Query: 82 LHPRFPEAPYVYAYRTVAEGGLRN-----QVVRLRHLGE-RGVLD-RVVLDGIPARPHGL 134 L P F E VY + AEGG ++ V R R + G+ D +V+L P G Sbjct: 102 LSPDFKEDRTVYL--SYAEGGGKDGTAGTAVGRGRLAADLSGLTDFKVILRQEPKLSTGN 159 Query: 135 HSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARP 194 H G R+AF DG L+VT GE +R AQDL L GK++R+ P+G NPF+G++G RP Sbjct: 160 HFGSRLAFDRDGYLFVTLGENNDRPTAQDLDKLQGKVVRIYPDGRVPDDNPFVGQQGVRP 219 Query: 195 EVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRVVGRGN- 253 E++S G RNPQGLA +P +G ++ +EHGP G DE+N+I G NYGWP N Sbjct: 220 EIWSYGQRNPQGLALNPWSGTIWENEHGPR-----GGDEINIIERGKNYGWPLATHGINY 274 Query: 254 ----DPRYR--------DPLYFWPQGFPPGNLAFFRGD--------LYVAGLRGQALLRL 293 P + P + W + +AF+ D +++ L Q L+RL Sbjct: 275 SLTPIPEAKGKTVEGTVPPHHVWEKSPGISGMAFYDADRFKPWQHNVFIGALATQELIRL 334 Query: 294 VLEGERGRWRVLRVETALSGF-GRLREVQVGPDGALYVTTSNRDG 337 +G+ +V+ E L G R+R+V+ GPDG LYV T DG Sbjct: 335 QFDGD----KVIHEERLLGGLKARIRDVRQGPDGFLYVLTDEEDG 375 Lambda K H 0.322 0.146 0.460 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: 510 Number of extensions: 42 Number of successful extensions: 6 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: 352 Length of database: 385 Length adjustment: 30 Effective length of query: 322 Effective length of database: 355 Effective search space: 114310 Effective search space used: 114310 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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