Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate Ac3H11_2201 PQQ-dependent oxidoreductase, gdhB family
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2201 Length = 383 Score = 182 bits (463), Expect = 1e-50 Identities = 132/351 (37%), Positives = 174/351 (49%), Gaps = 40/351 (11%) Query: 18 GQGLRVEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFRE-GRL--STYAELPVYHRGE 74 G + + V GL PWALAFLPDG L+ ERPGR+R+ G+L + PV G+ Sbjct: 36 GPAVSLVPVATGLANPWALAFLPDGQFLLTERPGRMRVVSATGQLGPALAGVPPVAAGGQ 95 Query: 75 SGLLGLALHPRFPEAPYVY-AYRTVAEGGLRN--QVVRLRHLGERGVLD--RVVLDGIPA 129 GLL + F +Y + +A G N V R + L RVV P Sbjct: 96 GGLLDVVTDADFARNRRIYFCFSELATSGAGNGTAVARATLAADAKSLQDVRVVFSQRPK 155 Query: 130 RPHGLHSGGRIAFGPDGMLYVTTGEVYER-ELAQDLASLGGKILRLTPEGEPAPGNPFLG 188 LH G RI PDG L+V GE Y R + AQ L + GK++R+TP+G PGNPF Sbjct: 156 VESALHFGCRIVQAPDGNLFVALGERYHRKDDAQKLDNHHGKVIRITPDGAVPPGNPFTN 215 Query: 189 RRGARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRV 248 + G PE++S GHRNPQG P G+L+ EHGP G DE+NL PG NYGWP + Sbjct: 216 QPGTLPEIWSYGHRNPQGATIGP-DGKLWMHEHGPQ-----GGDEINLPQPGRNYGWPVI 269 Query: 249 ----------VGRGN-DPRYRDPLYFWPQGFPPGNLAF---------FRGDLYVAGLRGQ 288 +G G PL+ W P +AF ++G L+V L+ Sbjct: 270 TYGENYGGGKMGEGTARAGMEQPLHHWTPSLAPSGMAFLTSTRYGAAWQGSLFVGSLKFG 329 Query: 289 ALLRLVLEGERGRWRVLRVETALSGFG-RLREVQVGPDGALYVTTSNRDGR 338 L RL + G ++ R E L G G R+R+V+ GPDG LY+ T + GR Sbjct: 330 TLHRLEVAG----GKLQREEKLLQGNGERIRDVRQGPDGLLYMVTDSPQGR 376 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: 579 Number of extensions: 50 Number of successful extensions: 8 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: 383 Length adjustment: 30 Effective length of query: 322 Effective length of database: 353 Effective search space: 113666 Effective search space used: 113666 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