Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate Synpcc7942_1791 Synpcc7942_1791 hypothetical protein
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__SynE:Synpcc7942_1791 Length = 411 Score = 166 bits (419), Expect = 1e-45 Identities = 123/352 (34%), Positives = 172/352 (48%), Gaps = 43/352 (12%) Query: 21 LRVEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFREGRL--STYAELP--VYHRGESG 76 + V +V GLE PW+LA+LP+G +LI ERPGR+RL R+G+L + A LP ++ +G+ G Sbjct: 56 VEVTPLVEGLEHPWSLAWLPNGDLLITERPGRLRLVRQGKLEPTAIAGLPADLFAQGQGG 115 Query: 77 LLGLALHPRFPEAPYVY-AYRTVAEGGLRNQVVRLRHLGERGVLDRVVLDGIPARPHGLH 135 LL +A+ P+F + +VY +Y E R QV R + G R V+ P + H Sbjct: 116 LLDIAVDPQFEQNRWVYFSYAAGTEAVNRVQVARGKLNGLRLENVEVIFTVRPDKSSAQH 175 Query: 136 SGGRIAFGPDGMLYVTTGEVYE----------RELAQDLASLGGKILRLTPEGEPAPGNP 185 G R+A+ PD L + G+ R AQ S GKI R+ +G NP Sbjct: 176 FGSRLAWLPDRTLLIAIGDGGNPPVELNGRLIRHQAQMPESGLGKIHRINRDGSIPADNP 235 Query: 186 FLGRRGARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGW 245 F + A+ ++SLGHRN QGLA PKTG ++S+EHG G DE+N I G NYGW Sbjct: 236 FRNQPKAQASLWSLGHRNIQGLAVDPKTGTVWSTEHG-----SRGGDELNQIKAGENYGW 290 Query: 246 PRVV------GRGNDPRYR-----DPLYFWPQGFPPGNLAFFR--------GDLYVAGLR 286 P V G P DP W P + +R G ++ GL Sbjct: 291 PEVTFSQEYWGAEITPLRTQAGMIDPHLVWTPAIAPSGITVYRGTKVPDWQGKIFAGGLV 350 Query: 287 GQALLRLVLEGERGRWRVLRVETALSGFGRLREVQVGPDGALYVTTSNRDGR 338 G+ + + L E V R+ R+R+V+ GP G LYV T G+ Sbjct: 351 GRDIRVIQLSPEGQATNVSRIPIG----ARVRDVRQGPSGDLYVLTDESSGK 398 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: 476 Number of extensions: 40 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: 411 Length adjustment: 30 Effective length of query: 322 Effective length of database: 381 Effective search space: 122682 Effective search space used: 122682 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: 50 (23.9 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