Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_086510147.1 BZY95_RS11910 PQQ-dependent sugar dehydrogenase
Query= BRENDA::I7A144 (352 letters) >NCBI__GCF_002151265.1:WP_086510147.1 Length = 416 Score = 186 bits (473), Expect = 7e-52 Identities = 129/364 (35%), Positives = 178/364 (48%), Gaps = 56/364 (15%) Query: 21 LRVEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFREGRLSTYAELPVYHRGES----- 75 L V +VVGG+E PWA+A+LPD MLI RPGR+ L ++ LP E Sbjct: 53 LTVTQVVGGIEHPWAVAWLPDERMLITARPGRLYLVDGDEVTEVGNLPKIDTDEDQLTAP 112 Query: 76 ------GLLGLALHPRFPEAPYVYAYRTVAEGGLRNQVVRLRHLGERGVLDRVVL--DG- 126 GLL + +HP + ++Y T + G + V+ G L R L DG Sbjct: 113 EGGNQGGLLDVVVHPDYENNGWIYF--TYSSPGDDDSVMGDDEYGTGTALARARLSDDGS 170 Query: 127 -----------IPARPHGLHSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLT 175 +P G H G RI F DG + + G+ R +QDL GG I+RL Sbjct: 171 ELTDLETIYAQVPRTAPGRHYGSRIVFPGDGSVMFSIGDRGIRYPSQDLTDPGGSIIRLH 230 Query: 176 PEGEPAPGNPFLGRR--GARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDE 233 +G GNPF+ RPE++S GHRN QGLA HP+TGEL++ +HGPSG G ++ Sbjct: 231 EDGGAFEGNPFIEAEPGNLRPEIFSYGHRNNQGLALHPETGELWAIDHGPSG----GGEQ 286 Query: 234 VNLIVPGGNYGWPRV-VGRGND-----------PRYRDPLYFWPQGFPPGNLAFFRGD-- 279 + + G N+GWP+V GR D P + P++ W P L F+ GD Sbjct: 287 LYVAEAGSNHGWPQVSFGREYDTDEFIGIGEVAPGVKPPVHVWEDTLAPSGLTFYTGDEF 346 Query: 280 ------LYVAGLRGQALLRLVLEGERGRWRVLRVETALSGFGRLREVQVGPDGALYVTTS 333 L++ L + L R+VL+GE + +E L GR+R+V+ GPDG LYV T Sbjct: 347 PGWQGNLFIGALYAERLHRVVLDGEAIAHEEILLENEL---GRIRDVRQGPDGLLYVLTD 403 Query: 334 NRDG 337 DG Sbjct: 404 ESDG 407 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: 626 Number of extensions: 45 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: 416 Length adjustment: 30 Effective length of query: 322 Effective length of database: 386 Effective search space: 124292 Effective search space used: 124292 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: 50 (23.9 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