Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate GFF2249 HP15_2199 glucose/sorbosone dehydrogenase
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__Marino:GFF2249 Length = 511 Score = 197 bits (501), Expect = 5e-55 Identities = 128/344 (37%), Positives = 176/344 (51%), Gaps = 39/344 (11%) Query: 23 VEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFRE----GRLSTYAELPVYHRGESGLL 78 VE + GLE PW+LAFLP GG L+ ER GR+R+ E G+ PV++ ++GL Sbjct: 173 VETLTSGLEHPWSLAFLPGGGALVTERAGRLRMISEEWELGQAPITGVPPVFNDAQAGLF 232 Query: 79 GLALHPRFPEAPYVYAYRTVAEGGLRNQVVRLRHLGERGVLDRV-VLDGIPARPHGLHSG 137 + L P F V+ + + V L + + V + PA+ H G Sbjct: 233 DVLLSPDFENNQLVFLAYSCGTASANHLCVARGQLQAEALTEVVEIFRAKPAKEGSAHYG 292 Query: 138 GRIAFGPDGMLYVTTGEVYE-RELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPEV 196 GR+A+ PDG L VT G+ ++ RE AQ+L+S GKI+RL P+G NPF+GR GA PE+ Sbjct: 293 GRMAWLPDGTLIVTLGDGFDYREQAQNLSSHLGKIVRLNPDGSVPADNPFVGREGALPEI 352 Query: 197 YSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRVVGRGND-- 254 YS GHRN QGL + L + EHGP G DE+N+I PG NYGWP V+ G D Sbjct: 353 YSYGHRNVQGLVFDSVENVLIAHEHGPR-----GGDEINIIEPGHNYGWP-VITHGIDYT 406 Query: 255 ----------PRYRDPLYFWPQGFPPGNLAFFRGDLY--------VAGLRGQALLRLVLE 296 PL W P + +RG+L+ V L +++ R+ LE Sbjct: 407 GAMITPFVEREGMEQPLLHWTPSIAPSGMTRYRGELFPDWQGNLLVGALADKSVHRVTLE 466 Query: 297 -GERGRWRVLRVETALSGFG-RLREVQVGPDGALYVTTSNRDGR 338 GE VE+ G R+R+V GPDGA+Y+ T + DGR Sbjct: 467 AGEAS-----DVESLFEAMGERIRDVATGPDGAVYLLTDSADGR 505 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: 576 Number of extensions: 39 Number of successful extensions: 8 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: 511 Length adjustment: 32 Effective length of query: 320 Effective length of database: 479 Effective search space: 153280 Effective search space used: 153280 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: 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