Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_094932674.1 CDO52_RS22395 PQQ-dependent sugar dehydrogenase
Query= BRENDA::I7A144 (352 letters) >NCBI__GCF_002263495.1:WP_094932674.1 Length = 382 Score = 252 bits (644), Expect = 1e-71 Identities = 153/337 (45%), Positives = 198/337 (58%), Gaps = 31/337 (9%) Query: 25 EVVGGLEVPWALAFLPDGGMLIAERPGR--IRLFREGRLSTYAELPVYH-RGESGLLGLA 81 +V LEVPW +AFLPDG L+ ER +R+ G ++ + RGE GLLGLA Sbjct: 63 DVATDLEVPWDIAFLPDGAALVTERDSARIVRVEPGGEVTEVGTVDAAAPRGEGGLLGLA 122 Query: 82 LHPRFPEAPYVYAYRTVAEGGLRNQVVRLRHLGERGVLD-RVVLDGIPARPHGLHSGGRI 140 +HP +P P +Y Y T A+ N+++R+ + + G+ + VVLDGIP +H+GGRI Sbjct: 123 VHPHYPADPAIYVYVTAADD---NRILRMSYAADSGLGEPEVVLDGIPKA--AVHNGGRI 177 Query: 141 AFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPEVYSLG 200 AFGPDG+LY +TG+ E AQD SLGGKILR+TP+G+ NPF VYS G Sbjct: 178 AFGPDGLLYASTGDATEGSTAQDTGSLGGKILRMTPDGKAPDDNPFGNL------VYSYG 231 Query: 201 HRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRVVGRGNDPRYRDP 260 HRN QGLAW + G LF++E G +DE+N+I PG NYGWP V G G D RY +P Sbjct: 232 HRNVQGLAWDDE-GRLFATEFGQD-----TYDEINVIEPGDNYGWPEVEGIGGDDRYTEP 285 Query: 261 LYFW-PQGFPPGNLAFFRGDLYVAGLRGQALLRLVLEGER----GRWRVLRVETALSGFG 315 + W P P A G L+VA LRG+ L ++ L G+ G L VE +G Sbjct: 286 VVVWRPAEASPSGGAIAGGALWVAALRGERLWKVPLTGDADDPVGDPEALYVER----YG 341 Query: 316 RLREVQVGPDGA-LYVTTSNRDGRGQVRPGDDRVLRL 351 RLR V P G L+V TSNRDGRG GDDR+LR+ Sbjct: 342 RLRSVTTAPGGTELWVGTSNRDGRGSPASGDDRILRV 378 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: 635 Number of extensions: 47 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: 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 24 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