Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_057508207.1 ABB28_RS08440 PQQ-dependent sugar dehydrogenase
Query= BRENDA::I7A144 (352 letters) >NCBI__GCF_001431535.1:WP_057508207.1 Length = 387 Score = 155 bits (392), Expect = 2e-42 Identities = 113/336 (33%), Positives = 162/336 (48%), Gaps = 42/336 (12%) Query: 33 PWALAFLPDGGMLIAERPGRIR---LFREGRLSTYAELPVYHRGESGLLGLALHPRFPEA 89 PWA+ FLPDG +L+ E+ GR++ L + V + G+ G + LHP F Sbjct: 56 PWAMTFLPDGSLLVTEKAGRLQHLDLTSRTKHEITGGPKVAYGGQGGFGDVVLHPDFASN 115 Query: 90 PYVY-AYRTVAEGGLRNQVVRLRHL-----GERGVLDRVVLDGIPARPHGL-HSGGRIAF 142 VY +Y R V L G + D V+ A+ G H G RIAF Sbjct: 116 QLVYLSYAEEGSNNTRGAAVARAKLVLDASGAGTLQDLSVIWRQDAKVSGNGHYGHRIAF 175 Query: 143 GPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPEVYSLGHR 202 GPDG L++T+ E + + AQD+AS GK++RL +G NPF + G +V+SLGHR Sbjct: 176 GPDGKLWITSSERQKFDPAQDMASNLGKLIRLNDDGSVPADNPFASQGGVAAQVWSLGHR 235 Query: 203 NPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRVVGRGND-------- 254 N G+A+ +L+ E GP+ G DE+NLI G NYG+P +V G+ Sbjct: 236 NMLGIAF-DANNKLWVHEMGPA-----GGDELNLITRGENYGYP-IVSNGDHYDGRPIPD 288 Query: 255 ----PRYRDPLYFWPQGFPPGNLAFFRGDL--------YVAGLRGQALLRLVLEGERGRW 302 P + P W P + GDL ++ GL QAL+R+ +GE R Sbjct: 289 HSTRPEFAAPKVTWNPVISPAGFIIYSGDLFPQWKGSGFIGGLSSQALVRVSFDGENAR- 347 Query: 303 RVLRVETALSGFGRLREVQVGPDGALYVTTSNRDGR 338 E G R+REV+ GPDGA++V ++G+ Sbjct: 348 ---EAERFDMG-ARIREVEQGPDGAVWVLEDGKNGK 379 Score = 23.5 bits (49), Expect = 0.010 Identities = 22/64 (34%), Positives = 27/64 (42%), Gaps = 16/64 (25%) Query: 119 LDRVVLDGIPARP-HGLHSGGRIAF---GPDGMLYVTTGEVYERELAQDLASLGGKILRL 174 L RV DG AR G RI GPDG ++V GK+L+L Sbjct: 336 LVRVSFDGENAREAERFDMGARIREVEQGPDGAVWVLED------------GKNGKLLKL 383 Query: 175 TPEG 178 TP+G Sbjct: 384 TPKG 387 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: 454 Number of extensions: 35 Number of successful extensions: 7 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: 387 Length adjustment: 30 Effective length of query: 322 Effective length of database: 357 Effective search space: 114954 Effective search space used: 114954 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 24 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