Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_066608672.1 V473_RS16930 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family
Query= BRENDA::D4P700 (796 letters) >NCBI__GCF_001046645.1:WP_066608672.1 Length = 778 Score = 606 bits (1562), Expect = e-177 Identities = 342/805 (42%), Positives = 461/805 (57%), Gaps = 54/805 (6%) Query: 12 RFLTVLFA---VLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYA 68 RFL + F +TGA + G L +GGS +Y+ G M+ A L WRR S +++++ Sbjct: 3 RFLNIAFLSSLTITGASLAWLGGRLLLLGGSPWYLASGIVMVAVALLGWRRRSVSILLFW 62 Query: 69 LLLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYR--GLYQPGKGA-LGAMGV 125 L L A L W WEVG D WALAPR + + G++++ PF R G QP GA L G+ Sbjct: 63 LYLAANLGWATWEVGADGWALAPRIAMPMGLGLYMLTPFYRRHVGRMQPLPGARLLWPGL 122 Query: 126 ALVASAAVLTYSVFNDPQVVNGALPATADNAPQAQ------PLSNIADGDWPAYARDQQG 179 AL+ + V L AD P + P + DGDW AY D+ G Sbjct: 123 ALILAGGV--------------GLAFWADRMPAPRSELWGPPPAQAGDGDWIAYGNDRGG 168 Query: 180 TRFSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITD-EVTPIKIRDTLYLCTPHQIL 238 +RFSPL QI NV L+ AW ++TG + D + T +V P+KI + LYLC + + Sbjct: 169 SRFSPLAQITPANVGHLRPAWTYRTGKL---GDGKQGTAFQVNPLKIGNRLYLCAGNNDV 225 Query: 239 FALDAATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVN 298 ALD TG+Q W+ +P + V CRGV+Y+ P A C+ RIY Sbjct: 226 IALDPETGRQLWRHNPKTDLAGVYGLV-CRGVTYYRVPQANGP-------CAERIYTATL 277 Query: 299 DGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDN 358 D RL ALDA TG CP FG G++DL+ G Y TSPP + +V+ G VTD Sbjct: 278 DARLIALDAATGRPCPGFGRGGQVDLRSGLGTVDKGYYFVTSPPALVRGRLVLGGWVTDG 337 Query: 359 FSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDI 418 EPSG IR FD +G W FD G D + +PA TFT +PNSWAP D L + Sbjct: 338 QRIGEPSGVIRAFDAVSGDFAWAFDIGRPDDHGLPAPGATFTPGTPNSWAPMSSDESLGL 397 Query: 419 VYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTL 478 VY P G TPD +GG+RT +R++SSV+AL+A TG + WS+QT HHDLWD D+P+QPTL Sbjct: 398 VYAPTGNATPDYFGGHRTANDDRFSSSVIALDAATGAVRWSFQTTHHDLWDYDVPAQPTL 457 Query: 479 ADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSATQPYSE 538 D+ V + P K G IF+LDR TGK ++P E PVPQGA G+ ++ TQPYS Sbjct: 458 VDLP----GGVRGLIQPTKRGEIFLLDRATGKPILPVEERPVPQGAVAGERIAKTQPYS- 512 Query: 539 LTFRPK---QNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPS-EQGTLVFPGNLGMF 594 T P T+K MWG T DQ +CR+ F++ R++G TP S E T+ +PG LG Sbjct: 513 -TTMPSFGGPRPTEKGMWGLTPIDQAICRIRFRQARFDGDMTPLSTEHPTITWPGYLGGI 571 Query: 595 EWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPY 654 +WGG+SVD R + I N + ++LIPR + G G Q GVPY Sbjct: 572 DWGGVSVDKLRGLMIVNNNQVGNYNRLIPRAEADRRGIKPMNAVHMGDVGGPAAQQGVPY 631 Query: 655 GVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPL----PFKMGM 710 ++ PFLSP +PC+QP +G ++AVD++T ++VW + +GT RDS P+ L P MG+ Sbjct: 632 AAQIAPFLSPLAIPCQQPPYGRINAVDIRTGKMVWSRTLGTSRDSGPLALPTLVPIPMGV 691 Query: 711 PMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTY--EVNGKQY 768 P +GG VATA + FIGAT ++ RAF T TG+LLW+ARLPAGG A+P +Y +G+Q+ Sbjct: 692 PNIGGSVATASGLTFIGATQEHAFRAFDTATGQLLWKARLPAGGNASPSSYWSSASGRQF 751 Query: 769 VVIAAGGHGSFGTKLGDYVIAYALP 793 +VIAAGGHG+ + D ++AYALP Sbjct: 752 IVIAAGGHGAMLSGSSDQLVAYALP 776 Lambda K H 0.319 0.137 0.433 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: 2281 Number of extensions: 157 Number of successful extensions: 19 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: 796 Length of database: 778 Length adjustment: 41 Effective length of query: 755 Effective length of database: 737 Effective search space: 556435 Effective search space used: 556435 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: 55 (25.8 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