Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate SMa0564 SMa0564 dehydrogenase
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__Smeli:SMa0564 Length = 367 Score = 176 bits (446), Expect = 9e-49 Identities = 134/344 (38%), Positives = 178/344 (51%), Gaps = 31/344 (9%) Query: 15 LARGQGLRVEEVVG-GLEVPWALAFLPDGGMLI-AERPGRIRLFREG---RLSTYAELPV 69 L RG+G V+ GL+ PW + + DG LI E+ G + + G R + P+ Sbjct: 44 LDRGEGAWSSSVLADGLDYPWDI--VRDGERLILTEKAGTVVIIEGGNVQRSTLQTSDPL 101 Query: 70 YHRGESGLLGLALHPRFPEAPYVYAYRTVAEGGL-RNQVVRLRHLGERGVLDRVVLDGIP 128 G +GLLG+AL P F ++ + Y + + G N++V R G V++D IP Sbjct: 102 RTEGGAGLLGIALAPDFADSGQAFFYYSYSSGSEPANRIVAARFDGNTWRETAVLVDAIP 161 Query: 129 ARPHGLHSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLG 188 H L++GGRIA GPD LYVTTG E QDL SL GK+LRLT G NPF G Sbjct: 162 G--HRLYNGGRIAIGPDDHLYVTTGWTENYERPQDLQSLAGKVLRLTLAGGVPEDNPFQG 219 Query: 189 RRGARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRV 248 VYS GHRNPQGLAW+ + GELF SEHG + DE+NLI PG NYGWP + Sbjct: 220 SL-----VYSFGHRNPQGLAWNAE-GELFVSEHGQA-----ALDEINLIAPGANYGWPII 268 Query: 249 VGRGNDPRYRDP-LYFWPQGFPPGNLAFFRGDLYVAGLRGQALLRLVLEGERGRWRVLRV 307 G + P ++ + P +AF +L V L+G+ L L + R L+ Sbjct: 269 SGDETQEGMQPPFVHSGGDTWAPSGIAFAGNELLVTALQGRGLYVLDRQA-----RTLQP 323 Query: 308 ETALSGFGRLREVQVGPDGALYVTTSNRDGRGQVRPGDDRVLRL 351 +L R+R V D L +TT NR RGQ P DR++RL Sbjct: 324 VVSLG--ERVRHVLPVGDDLLLITT-NRSPRGQ-GPSKDRLVRL 363 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: 479 Number of extensions: 35 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: 367 Length adjustment: 29 Effective length of query: 323 Effective length of database: 338 Effective search space: 109174 Effective search space used: 109174 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