Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_086511877.1 BZY95_RS21205 PQQ-dependent sugar dehydrogenase
Query= BRENDA::I7A144 (352 letters) >NCBI__GCF_002151265.1:WP_086511877.1 Length = 384 Score = 183 bits (465), Expect = 6e-51 Identities = 125/343 (36%), Positives = 178/343 (51%), Gaps = 37/343 (10%) Query: 21 LRVEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFREGRLSTYAE-LP-VYHRGESGLL 78 LR+E + GLE PWA+A LPDG L+ ERPGR+ L E T+ E +P V +G+ GLL Sbjct: 44 LRLERIAEGLENPWAVAMLPDGRFLVTERPGRLALIDEDGSITHLEGVPEVSAQGQGGLL 103 Query: 79 GLALHPRFPEAPYVYAYRTVA---EGGLRNQVVRLRHLGERGVLD-RVVLDGIPARPHGL 134 + LHPR+ + + + Y T + +GG + R R L + + D + + G Sbjct: 104 DVTLHPRYGDGEHDWLYFTWSKPGDGGTATALSRAR-LSDDALSDVETLFEQDRFSGPGR 162 Query: 135 HSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARP 194 H G R+A+ PD L +T G+ E AQ G +LRL +G NPF Sbjct: 163 HYGSRLAWLPDETLLMTIGDRGTPERAQAADDHAGSVLRLAADGSAPDDNPFADDDATLA 222 Query: 195 EVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRV------ 248 E+Y+LG+RN QG+ + GE++++EHGP +G DE+NLIV G NYGWP V Sbjct: 223 EIYTLGNRNIQGMV-VTEQGEIWATEHGP-----FGGDELNLIVAGENYGWPEVSQGRDY 276 Query: 249 -----VGRGNDPRYRDPLYFWPQGFPPGNLA--------FFRGDLYVAGLRGQALLRLVL 295 +G + P +DP++ + F P LA ++GDL GLRG+ L RL + Sbjct: 277 GTREPIGEDSLPGMQDPIHVFEAPFAPSGLAQVTSVTFGEWQGDLLAGGLRGERLYRLSI 336 Query: 296 EGERGRWRVLRVETALSG-FGRLREVQVGPDGALYVTTSNRDG 337 EGE ++ E L G GR+R V G DGA+Y+ G Sbjct: 337 EGE----QLADSEVVLDGHIGRIRGVHQGHDGAIYLVNDEAQG 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: 528 Number of extensions: 37 Number of successful extensions: 9 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: 384 Length adjustment: 30 Effective length of query: 322 Effective length of database: 354 Effective search space: 113988 Effective search space used: 113988 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