Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate Pf6N2E2_801 Soluble aldose sugar dehydrogenase, PQQ-dependent (EC 1.1.5.-)
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_801 Length = 382 Score = 179 bits (453), Expect = 1e-49 Identities = 125/347 (36%), Positives = 180/347 (51%), Gaps = 39/347 (11%) Query: 21 LRVEEVVGGLEVPWALAFLP-DGGMLIAERPGRIRLFR-EGRLST-YAELP-VYHRGESG 76 L V VV GLE PW++AFLP GML+ ERPG +R+ +G+LS + +P V+ +G+ G Sbjct: 37 LEVTTVVKGLEHPWSVAFLPGQQGMLVTERPGNLRVVSADGQLSAPLSGVPEVWAKGQGG 96 Query: 77 LLGLALHPRFPEAPYVY-AYRTVAEGGLRNQVVRLRHLGE--RGVLD-RVVLDGIPARPH 132 LL + L P F + VY +Y G V L E + + + V+ +P Sbjct: 97 LLDVVLSPDFKQDRTVYLSYAEAGADGKAGTAVGRGQLSEDLKSLKNFDVIFRQLPKLST 156 Query: 133 GLHSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGA 192 G H G R+ F DG L++T GE ER AQDL L GKI+R+ P+G+ NPF+G++ Sbjct: 157 GNHFGSRLVFDRDGYLFITLGENNERPTAQDLDKLQGKIVRIYPDGKVPDDNPFVGQKNV 216 Query: 193 RPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWP------ 246 RPE++S G RNPQG A +P G L+ +EHGP G DE+N+I G NYGWP Sbjct: 217 RPEIWSYGMRNPQGAALNPWNGTLWENEHGPK-----GGDEMNIIERGKNYGWPLATHGI 271 Query: 247 ------------RVVGRGNDPRY---RDPLYFWPQGFPPGNLAFFRGDLYVAGLRGQALL 291 + V G DP + P + G ++ ++++ L L+ Sbjct: 272 NYSGAPIPEAQGKTVEGGLDPHHVWQVSPGLSGMAFYDHGRFKAWQHNVFIGALVPGELI 331 Query: 292 RLVLEGERGRWRVLRVETALSGF-GRLREVQVGPDGALYVTTSNRDG 337 RL L+ + +++ E L R+R+V+ GPDG LYV T DG Sbjct: 332 RLQLQDD----KIVHEERLLGELKARIRDVRQGPDGYLYVLTDEDDG 374 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: 493 Number of extensions: 36 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: 352 Length of database: 382 Length adjustment: 30 Effective length of query: 322 Effective length of database: 352 Effective search space: 113344 Effective search space used: 113344 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