Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate 14962 b0837 predicted dehydrogenase (NCBI)
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__Keio:14962 Length = 371 Score = 169 bits (429), Expect = 8e-47 Identities = 123/365 (33%), Positives = 183/365 (50%), Gaps = 42/365 (11%) Query: 6 FLVGLLGLGLARGQG---LRVEEVVGGLEVPWALAFLPDG-GMLIAERPGRIRLFREGR- 60 FLV L+ L A + VE + L+ PWALAFLPD GMLI R G +R ++ G+ Sbjct: 7 FLVPLICLSSALWAAPATVNVEVLQDKLDHPWALAFLPDNHGMLITLRGGELRHWQAGKG 66 Query: 61 -LSTYAELP-VYHRGESGLLGLALHPRFPEAPYVY-AYRTVAEGGLRNQVVRLRHLGE-- 115 + + +P V+ G+ GLL + L P F ++ ++ +Y V + G V L + Sbjct: 67 LSAPLSGVPDVWAHGQGGLLDVVLAPDFAQSRRIWLSYSEVGDDGKAGTAVGYGRLSDDL 126 Query: 116 RGVLD-RVVLDGIPARPHGLHSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRL 174 V D R V +P G H GGR+ F G L++ GE +R AQDL L GK++RL Sbjct: 127 SKVTDFRTVFRQMPKLSTGNHFGGRLVFDGKGYLFIALGENNQRPTAQDLDKLQGKLVRL 186 Query: 175 TPEGEPAPGNPFLGRRGARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEV 234 T +GE NPF+ GAR E++S G RNPQG+A +P + L+ +EHGP G DE+ Sbjct: 187 TDQGEIPDDNPFIKESGARAEIWSYGIRNPQGMAMNPWSNALWLNEHGPR-----GGDEI 241 Query: 235 NLIVPGGNYGWPRVVGRGNDPRYR-------------DPLYFWPQGFPPGNLAFFRGD-- 279 N+ G NYGWP N ++ P+++W +AF+ D Sbjct: 242 NIPQKGKNYGWPLATWGINYSGFKIPEAKGEIVAGTEQPVFYWKDSPAVSGMAFYNSDKF 301 Query: 280 ------LYVAGLRGQALLRLVLEGERGRWRVLRVETALSGFG-RLREVQVGPDGALYVTT 332 L++ L+ + ++ + + G+ +V L+ G R+R+V+ GPDG LYV T Sbjct: 302 PQWQQKLFIGALKDKDVIVMSVNGD----KVTEDGRILTDRGQRIRDVRTGPDGYLYVLT 357 Query: 333 SNRDG 337 G Sbjct: 358 DESSG 362 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: 422 Number of extensions: 28 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: 371 Length adjustment: 29 Effective length of query: 323 Effective length of database: 342 Effective search space: 110466 Effective search space used: 110466 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