Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate Pf1N1B4_4753 Soluble aldose sugar dehydrogenase, PQQ-dependent (EC 1.1.5.-)
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4753 Length = 383 Score = 193 bits (490), Expect = 7e-54 Identities = 133/348 (38%), Positives = 183/348 (52%), Gaps = 40/348 (11%) Query: 21 LRVEEVVGGLEVPWALAFLPDG-GMLIAERPGRIRLFR-EGRLSTYAE-LP-VYHRGESG 76 L + +V GL+ PW+LAFLPD GML+ ERPG +RL +G+LS +P V+ +G+ G Sbjct: 37 LELTPIVKGLDHPWSLAFLPDRQGMLVTERPGNLRLVSADGKLSGPLNGVPQVWAKGQGG 96 Query: 77 LLGLALHPRFPEAPYVYAYRTVA--EGGLRNQVVRLRHLGE--RGVLD-RVVLDGIPARP 131 LL + L P F + VY EGG V L E + D RV+ P Sbjct: 97 LLDVVLSPDFKQDRMVYLSYAEGGGEGGKAGTAVGRGRLSEDLTAIKDFRVIFRQEPKLS 156 Query: 132 HGLHSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRG 191 G H G R+ F DG L++T GE +R AQDL L GKI+RL P+G+ NPF+G++G Sbjct: 157 VGNHFGSRLVFDRDGYLFITLGENNDRPTAQDLDKLQGKIVRLYPDGKVPEDNPFVGQKG 216 Query: 192 ARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRVVGR 251 RPE++S G RNPQG A +P +G L+ +EHGP G DE+N+I G NYGWP Sbjct: 217 VRPEIWSYGQRNPQGAALNPWSGTLWENEHGPR-----GGDEINIIERGKNYGWPMATHG 271 Query: 252 GN-----DPRYR--------DPLYFWPQGFPPGNLAFFRGD--------LYVAGLRGQAL 290 N P + P + W + +AF+ GD +++ L Q L Sbjct: 272 INYTGLPIPEAKGETAEGTVGPHHVWEKSPGLSGMAFYDGDRFKAWQHNVFIGALVSQEL 331 Query: 291 LRLVLEGERGRWRVLRVETALSGFG-RLREVQVGPDGALYVTTSNRDG 337 +RL EG+ +V+ E L R+R+V+ GPDG LY+ T DG Sbjct: 332 IRLQFEGD----KVVHEERLLGELNKRIRDVRQGPDGYLYLLTDEDDG 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: 490 Number of extensions: 39 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: 383 Length adjustment: 30 Effective length of query: 322 Effective length of database: 353 Effective search space: 113666 Effective search space used: 113666 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