Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate WP_071884227.1 BN137_RS05740 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase
Query= CharProtDB::CH_002195 (796 letters) >NCBI__GCF_000319285.1:WP_071884227.1 Length = 798 Score = 1444 bits (3737), Expect = 0.0 Identities = 673/798 (84%), Positives = 736/798 (92%), Gaps = 2/798 (0%) Query: 1 MAINNTGSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRS 60 MA RLLV LTALFAAL GLYLL+GG WLV+IGGSWYYPIAG+ ML AW+LW+ Sbjct: 1 MAETKKTQSRLLVILTALFAALSGLYLLVGGIWLVSIGGSWYYPIAGVGMLATAWLLWKR 60 Query: 61 KRAALWLYAALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGA 120 AALWLYA +LLGTM WG+WEVGFDFWALTPR DILVFFG+WLILPFVWRRL P+ Sbjct: 61 NAAALWLYAIILLGTMAWGIWEVGFDFWALTPRCDILVFFGVWLILPFVWRRLHTPSRAG 120 Query: 121 VAALVVALLISGGILTWAGFNDPQEINGTLSADATPA--EAISPVADQDWPAYGRNQEGQ 178 V AL+V+L+I+ G+L WAGFNDPQE+NGTLSAD+TPA + D DWPAYGRNQEGQ Sbjct: 121 VPALLVSLIITAGLLFWAGFNDPQEVNGTLSADSTPAAVNGSQDIPDGDWPAYGRNQEGQ 180 Query: 179 RFSPLKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFA 238 R+SPLKQIN DNVH LKEAWVFRTGD+K PNDPGEITNEVTPIKVGDTL+LCTAHQRLFA Sbjct: 181 RYSPLKQINTDNVHQLKEAWVFRTGDLKLPNDPGEITNEVTPIKVGDTLFLCTAHQRLFA 240 Query: 239 LDAASGKEKWHYDPELKTNESFQHVTCRGVSYHEAKAETASPEVMADCPRRIILPVNDGR 298 +DAA+GKEKWH+DP+L TN +FQHVTCRGVSYHEA ASP+V+ADCPRRIILPVNDGR Sbjct: 241 VDAATGKEKWHFDPQLNTNPTFQHVTCRGVSYHEATTANASPDVVADCPRRIILPVNDGR 300 Query: 299 LIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSVTDNFST 358 L A+NA+NGKLCE+FANKG+LNLQ+NMP T PG+YEPTSPPI+TDK IV+AG+VTDNFST Sbjct: 301 LFAVNADNGKLCESFANKGILNLQTNMPVTTPGMYEPTSPPIVTDKVIVIAGAVTDNFST 360 Query: 359 RETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKLDLVYL 418 RE SGVIRGFD+NTG+LLWAFDPGAKDPNAIP+DEH F+ NSPNSWAPA+YDAKLD+VYL Sbjct: 361 REPSGVIRGFDINTGKLLWAFDPGAKDPNAIPADEHHFSLNSPNSWAPASYDAKLDIVYL 420 Query: 419 PMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPAQPTLADI 478 PMGVTTPDIWGGNRTPEQERYAS+I+ALNA+TGKL WSYQTVHHDLWDMDLPAQPTLADI Sbjct: 421 PMGVTTPDIWGGNRTPEQERYASAIVALNASTGKLVWSYQTVHHDLWDMDLPAQPTLADI 480 Query: 479 TVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPTQPFSELSFR 538 TV G+ VPVIYAPAKTGNIFVLDRRNG+LVVPAPEKPVPQGAAKGDYVTPTQPFS+LSFR Sbjct: 481 TVKGETVPVIYAPAKTGNIFVLDRRNGKLVVPAPEKPVPQGAAKGDYVTPTQPFSDLSFR 540 Query: 539 PTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGMFEWGGISVD 598 P KDLSGADMWGATM+DQLVCRVMFH +RYEGIFTPPSEQGTLVFPGNLGMFEWGG++VD Sbjct: 541 PKKDLSGADMWGATMYDQLVCRVMFHSLRYEGIFTPPSEQGTLVFPGNLGMFEWGGLAVD 600 Query: 599 PNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGVPYGVTLNPFLS 658 P+R+VAIANPMALPFVSKLIPRGPGNPMEQPKDA+GTG+ESGIQPQYGVP+GVTLNPFLS Sbjct: 601 PHRQVAIANPMALPFVSKLIPRGPGNPMEQPKDAQGTGSESGIQPQYGVPFGVTLNPFLS 660 Query: 659 PFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLGGPIST 718 PFGLPCKQPAWGYISALDLKTNEVVWKKRIGTP+DSMPFPMP PVPFNMGMPMLGGPI+T Sbjct: 661 PFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPRDSMPFPMPFPVPFNMGMPMLGGPITT 720 Query: 719 AGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYEVNGKQYVVISAGGHGSF 778 GNVLFI ATADNYLRAYN++NGEKLW+ RLPAGGQATPMTYEVNGKQYVV+SAGGHGSF Sbjct: 721 GGNVLFIGATADNYLRAYNVTNGEKLWEARLPAGGQATPMTYEVNGKQYVVLSAGGHGSF 780 Query: 779 GTKMGDYIVAYALPDDVK 796 GTKMGDYIVAYALPDD K Sbjct: 781 GTKMGDYIVAYALPDDAK 798 Lambda K H 0.319 0.137 0.436 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: 2725 Number of extensions: 152 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: 796 Length of database: 798 Length adjustment: 41 Effective length of query: 755 Effective length of database: 757 Effective search space: 571535 Effective search space used: 571535 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