Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate AZOBR_RS31355 AZOBR_RS31355 putative glucose dehydrogenase precursor
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__azobra:AZOBR_RS31355 Length = 386 Score = 186 bits (471), Expect = 1e-51 Identities = 131/357 (36%), Positives = 182/357 (50%), Gaps = 55/357 (15%) Query: 23 VEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFR-EGRLSTYAE-LP-VYHRGESGLLG 79 V+ V GL PW LAFLPDG ML+ E+ GR+R+ +G +S + +P V RG+ GLL Sbjct: 38 VKTVASGLSHPWGLAFLPDGRMLVTEKDGRLRIVAPDGTVSAPVKGVPKVDDRGQGGLLD 97 Query: 80 LALHPRFPEAPYVYAYRTV--AEGGLRNQVVRLRHLGERGVLD---------RVVLDGIP 128 +AL P F + +VY + E G + V RGVL+ RV+ P Sbjct: 98 VALDPEFAQNRFVYLSFSEPGTEDGTNSTAVA------RGVLNADETALTDVRVIFSQKP 151 Query: 129 ARPHGLHSGGRIAFGPDGMLYVTTGE---VYERELAQDLASLGGKILRLTPEGEPAPGNP 185 +H G R+ F G LYVT GE R AQDL S GK++R+ +G NP Sbjct: 152 KVESRMHYGSRLVFDRQGHLYVTLGERSLEQFRTQAQDLDSHLGKVVRINRDGSVPADNP 211 Query: 186 FLGRRGARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGW 245 F+ + GA PE++S GHRN QG A +P+TG L+ +EHGP G DEVN+ PG NYGW Sbjct: 212 FVNQSGALPEIWSYGHRNIQGAALNPQTGALWINEHGPR-----GGDEVNVPEPGKNYGW 266 Query: 246 PRV------------VGRGNDPRYRDPLYFWPQGFPPGNLAFF--------RGDLYVAGL 285 P V G+ + P +P+Y W + F+ +G L+ GL Sbjct: 267 PVVSYGVNYNGTPIGTGKSSAPGMEEPVYQWTPVIGSSGMTFYTADTLPGWKGSLFNGGL 326 Query: 286 RGQALLRLVLEGERGRWRVLRVETALSGFG-RLREVQVGPDGALYVTTSNRDGRGQV 341 + ++RL L+G +V E G R+R+V GPDGALY+ T + RG++ Sbjct: 327 ATKEVVRLELDGN----KVKHEERMFRDLGKRIRQVSQGPDGALYLLTD--ENRGEI 377 Score = 29.3 bits (64), Expect = 2e-04 Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 12/42 (28%) Query: 139 RIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEP 180 +++ GPDG LY+ T E G+ILR+TP G+P Sbjct: 357 QVSQGPDGALYLLTDENR------------GEILRVTPAGKP 386 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: 484 Number of extensions: 41 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 352 Length of database: 386 Length adjustment: 30 Effective length of query: 322 Effective length of database: 356 Effective search space: 114632 Effective search space used: 114632 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