Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate GFF2859 Psest_2915 Glucose/sorbosone dehydrogenases
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__psRCH2:GFF2859 Length = 382 Score = 186 bits (472), Expect = 9e-52 Identities = 129/348 (37%), Positives = 182/348 (52%), Gaps = 43/348 (12%) Query: 23 VEEVVGGLEVPWALAFLPDGG-MLIAERPGRIRLFR-EGRLSTYAE-LP-VYHRGESGLL 78 V E+ G E PWALAFLPDG ML+ ERPGR+RL +G S E +P V+ + + GLL Sbjct: 37 VREIAAGFENPWALAFLPDGEHMLVTERPGRLRLVGLDGSRSKPLEGVPEVFAQAQGGLL 96 Query: 79 GLALHPRFPEAPYVYAYRTVAEGGLRNQ----VVRLRHLGERGVLDR--VVLDGIPARPH 132 + L P F VY T AE G + + V R R + L+ V+ +P Sbjct: 97 DVRLSPDFESDRLVYL--TYAEAGEQGKAGTAVGRGRLSDDHSKLENFEVIFRQLPKLST 154 Query: 133 GLHSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGA 192 G+H G R+ F DG L+V GE +R +QDL GK++R+ +G NPF+G+ G Sbjct: 155 GIHFGSRLVFDNDGHLFVALGENNQRPTSQDLDKHQGKVVRIGLDGSVPDDNPFIGQEGV 214 Query: 193 RPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRVVGRG 252 RPE++S GHRN QG A +P +G L+++EHGP G DEVN+ G NYGWP Sbjct: 215 RPEIWSYGHRNQQGAALNPWSGVLWTNEHGPR-----GGDEVNIPQAGKNYGWPLATHGI 269 Query: 253 NDPRY-------------RDPLYFWPQGFPPGNLAFFRGD--------LYVAGLRGQALL 291 N P + W + +AF+ G+ L++ L Q+L+ Sbjct: 270 NYSMLPIPEAKGKAVEGTEQPHHVWGKSPGVSGMAFYDGERFAAWQHSLFIGALVDQSLI 329 Query: 292 RLVLEGERGRWRVLRVETALSGFG-RLREVQVGPDGALYVTTSNRDGR 338 RL L+G+ R++ E L G R+R+V+VGPDG +Y+ T DG+ Sbjct: 330 RLRLDGD----RIVGEERLLKDLGARIRDVRVGPDGYVYLLTDAGDGK 373 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: 459 Number of extensions: 39 Number of successful extensions: 5 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 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