Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate CA265_RS06300 CA265_RS06300 glucose dehydrogenase
Query= BRENDA::Q8ZUN8 (371 letters) >FitnessBrowser__Pedo557:CA265_RS06300 Length = 362 Score = 202 bits (514), Expect = 1e-56 Identities = 126/349 (36%), Positives = 190/349 (54%), Gaps = 32/349 (9%) Query: 30 PSEEWKFKISEVASDLEVPWSIAPLGGGRYLVTERPGRLVLISPSGKKLVASFDVANV-- 87 P + K K+ + S L +PW + TE+ G++ ++P+ ++ + V Sbjct: 31 PDVDLKSKV--IVSGLSLPWEMVYGPDNFIWFTEKAGKISRLNPANGQVTPLLTITEVRT 88 Query: 88 -GEAGLLGLALHPEFPKKSWVYLYASYFAEGGHIRNRVIRGRLDGSTFKLKEVKTLIDGI 146 GE GLLG+ LHP+F +VY+ Y G + +V+R G +V L+D I Sbjct: 89 NGEGGLLGMTLHPDFAGNPYVYVVYGY---GSTYKAKVVRYTYSGGGLTSPQV--LLDQI 143 Query: 147 PGAYIHNGGRIRFGPDGMLYITTGDAADPRLAQDLSSLAGKILRVDEEGRPPADNPFPNS 206 P A IHNG R+ G L+I+TGDAAD Q+++SLAGKILR++ +G PADNP+PN+ Sbjct: 144 PAASIHNGSRLLIS-GGKLFISTGDAADTGNPQNVNSLAGKILRINLDGTIPADNPYPNN 202 Query: 207 PIWSYGHRNPQGIDWHRASGVMVATEHGPVGHDEVNIILKGGNYGWPLATG---KAGRGE 263 P+WS GHRN QG+ + + ++EHGP DE+NII KG NYGWP G ++G Sbjct: 203 PLWSLGHRNAQGL--IQVGNKIFSSEHGPDSDDEINIIEKGRNYGWPNIKGYCNESGEQS 260 Query: 264 F------VDPVIDTGSETWAPSGASFVHGDMFPGLRGWLLIACLRGSMLAAVNFGD-NME 316 F +P+I+ + T APSG ++ + D P + LL+A L+G+ L + D + Sbjct: 261 FCSSNNVAEPLIN-WTPTIAPSGLAYYNSDYIPQFKNSLLLAVLKGTKLMQLKLDDAQTK 319 Query: 317 VRKISTFFKNVFGRLRDVVIDDDGGILISTSNRDGRGSLRAGDDKILKI 365 + F+ N +GR+R + +G I I TSN DDKI++I Sbjct: 320 ITGTKDFYVNTYGRIRAICQSPEGKIYICTSN--------GSDDKIVEI 360 Lambda K H 0.320 0.140 0.432 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: 377 Number of extensions: 18 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: 371 Length of database: 362 Length adjustment: 30 Effective length of query: 341 Effective length of database: 332 Effective search space: 113212 Effective search space used: 113212 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 (21.7 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