Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_048080684.1 EJ01_RS13355 PQQ-dependent sugar dehydrogenase
Query= BRENDA::Q8ZUN8 (371 letters) >NCBI__GCF_000745485.1:WP_048080684.1 Length = 347 Score = 250 bits (638), Expect = 5e-71 Identities = 147/368 (39%), Positives = 218/368 (59%), Gaps = 27/368 (7%) Query: 1 MRRRTFLTLAVLVSLSASLGLLTAL--IRKGPSEEWKFKISEVASDLEVPWSIAPLGGGR 58 M+R+T V++ + L +++AL I P+ + ++ + DL PW+I L G+ Sbjct: 1 MKRKT-----VIIIIFVFLIIISALYFIIPKPANQQGYETEILVQDLNTPWAIDFLPDGK 55 Query: 59 YLVTERPGRLVLISPSGKKLVASFDVANVGEAGLLGLALHPEFPKKSWVYLYASYFAEGG 118 + TER GR+ + K V + V +GE+G+LG+A+ PEF ++YLY Y G Sbjct: 56 MIFTERDGRVSIFDNGTTKTVGTITVTQIGESGMLGIAVDPEFNTNKFIYLY--YTGANG 113 Query: 119 HIRNRVIRGRLDGSTFKLKEVKTLIDGIPGAYIHNGGRIRFGPDGMLYITTGDAADPRLA 178 NR+ R L+G+ LK LID IP A HNGGR++FG DG LY TTGDA + + A Sbjct: 114 ---NRISRFTLNGT---LKNETVLIDRIPNAQFHNGGRLKFGSDGKLYATTGDATNNQSA 167 Query: 179 QDLSSLAGKILRVDEEGRPPADNPFPNSPIWSYGHRNPQGIDWHRASGVMVATEHGPVGH 238 QD++SL GKILRV+++G P+DNPF N +++YG R+PQGI W + M ++HG + Sbjct: 168 QDINSLGGKILRVNKDGTVPSDNPFRNY-VYAYGLRDPQGITWDPLTKEMYLSDHGATRN 226 Query: 239 DEVNIILKGGNYGWPLATGKAGRGEFVDPVIDTGSETWAPSGASFVHGDMFPGLRGWLLI 298 DE+NII KGGNYGWP+ G ++ P+ T APSG ++ +G ++ + Sbjct: 227 DEINIITKGGNYGWPIYQGNESAQGYIKPLSVYTDFTLAPSGIAYYNGALY--------V 278 Query: 299 ACLRGSMLAAVNFG-DNMEVRKISTFFKNVFGRLRDVVIDDDGGILISTSNRDGRGSLRA 357 A LRGS L + + V F ++ GR+R+VV+ DG + I+TSNRDGRG ++ Sbjct: 279 AGLRGSQLRKITLSIEGNSVTGQEALFTSL-GRIREVVV-HDGYMYIATSNRDGRGVPQS 336 Query: 358 GDDKILKI 365 GDDKI++I Sbjct: 337 GDDKIIRI 344 Lambda K H 0.320 0.140 0.432 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: 357 Number of extensions: 22 Number of successful extensions: 4 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: 371 Length of database: 347 Length adjustment: 29 Effective length of query: 342 Effective length of database: 318 Effective search space: 108756 Effective search space used: 108756 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 (21.7 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