Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate PP_2198 PP_2198 aldose sugar dehydrogenase
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__Putida:PP_2198 Length = 381 Score = 191 bits (484), Expect = 3e-53 Identities = 131/348 (37%), Positives = 182/348 (52%), Gaps = 41/348 (11%) Query: 21 LRVEEVVGGLEVPWALAFLPDG-GMLIAERPGRIRLFR-EGRLS-TYAELP-VYHRGESG 76 L V+ + GL PWALAFLP G ML+ ER G +RL EG++ + + +P V+ G+ G Sbjct: 35 LIVDTLADGLRNPWALAFLPGGKDMLVTERAGNLRLVNAEGKVGPSISGVPKVWAEGQGG 94 Query: 77 LLGLALHPRFPEAPYVY-AYRTVAEGGLRNQVVRLRHLGE-RGVLDR--VVLDGIPARPH 132 LL +AL P F + VY +Y G V L E R L+ V+ P Sbjct: 95 LLDVALSPEFGKDRTVYLSYAEEGSDGKAGTAVGRGQLSEDRARLENFTVIFRQQPKLSV 154 Query: 133 GLHSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGA 192 G H G R+ F DG L++ GE +R AQDL L GK++R+ P+GE NPF+G+ Sbjct: 155 GNHFGSRLVFDRDGYLFIALGENNQRPTAQDLDKLQGKVVRILPDGEVPKDNPFVGKDNV 214 Query: 193 RPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGW------- 245 RPE++S GHRN QG A +P TG+L++ EHGP G DE+N+ PG NYGW Sbjct: 215 RPEIWSYGHRNQQGAALNPWTGQLWTHEHGPR-----GGDEINIPKPGKNYGWPIATHGI 269 Query: 246 -------PRVVGRGNDPRYRDPLYFWPQGFPPGNLAFFRG--------DLYVAGLRGQAL 290 P G D DP + W + +AF+ +L++ L Q L Sbjct: 270 NYSLLPIPEAKGEHVDGMV-DPHHVWEKSPGISGMAFYDSPTFKAWDHNLFIGALATQEL 328 Query: 291 LRLVLEGERGRWRVLRVETALSGF-GRLREVQVGPDGALYVTTSNRDG 337 +RL L+G+ +V+ E L R+R+V+VGPDG LYV T ++DG Sbjct: 329 IRLQLDGD----KVVHEERLLGDLKARIRDVRVGPDGYLYVLTDDKDG 372 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: 498 Number of extensions: 33 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: 381 Length adjustment: 30 Effective length of query: 322 Effective length of database: 351 Effective search space: 113022 Effective search space used: 113022 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