Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate SM_b20301 SM_b20301 dehydgrogenase
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__Smeli:SM_b20301 Length = 376 Score = 179 bits (455), Expect = 8e-50 Identities = 122/341 (35%), Positives = 174/341 (51%), Gaps = 36/341 (10%) Query: 23 VEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFR-EGRLSTYAE-LP-VYHRGESGLLG 79 VE GGLE PW A LPDG ML+ ERPGR+RL EG + E +P V+ +G+ GLL Sbjct: 39 VEVFAGGLEHPWGAALLPDGDMLVTERPGRLRLVSAEGAVGEPIEGVPDVFAQGQGGLLD 98 Query: 80 LALHPRFPEAPYVY-AYRTVAEGGLRNQVVRLRHLGERGVLD--RVVLDGIPARPHGLHS 136 +AL P F VY ++ EGG V R R + L +++ PA H Sbjct: 99 VALDPDFATNRTVYLSFAEEREGGAATSVGRGRLNDDATALSDFKIIFRQEPAASGENHF 158 Query: 137 GGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPEV 196 G R+AF PDG L++T GE ++ + AQD A+ G I+RL P+G NPF+GR GA E+ Sbjct: 159 GSRLAFAPDGKLFITLGERFDMQEAQDPANHLGTIVRLNPDGSIPDDNPFVGREGA-DEI 217 Query: 197 YSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWP---------- 246 +S GHRN Q A HP+T L+++E GP G DE+N+ G NYGWP Sbjct: 218 WSYGHRNVQSAAIHPETDVLWTAEMGP-----MGGDELNIPEAGKNYGWPAVSWGRHYTG 272 Query: 247 -RVVGRGNDPRYRDPLYFWPQGFPPGNLAFF--------RGDLYVAGLRGQALLRLVLEG 297 R+ + P + ++ W P + F+ RGDL + GL ++R+ +G Sbjct: 273 ERIPDPPSRPEFAGSIHSWTPVISPSGMMFYTGDLFADWRGDLLIGGLSVGGIVRVQTDG 332 Query: 298 ERGRWRVLRVETALSGFGRLREVQVGPDGALYVTTSNRDGR 338 ++ + E LS R+R++ DG++ GR Sbjct: 333 QK-----VTGEEVLSLEARIRDLLQASDGSVLALIDAASGR 368 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: 502 Number of extensions: 35 Number of successful extensions: 6 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: 376 Length adjustment: 29 Effective length of query: 323 Effective length of database: 347 Effective search space: 112081 Effective search space used: 112081 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