Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_052236884.1 FPB0191_RS08270 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase
Query= BRENDA::D4P700 (796 letters) >NCBI__GCF_000807275.1:WP_052236884.1 Length = 803 Score = 718 bits (1853), Expect = 0.0 Identities = 363/802 (45%), Positives = 503/802 (62%), Gaps = 26/802 (3%) Query: 9 SVVRFLTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYA 68 +V+ L L ++ G +L GGIWL ++GGS YY++ GA M+ A L++R N ALV+YA Sbjct: 5 NVLSTLVGLILIVMGVVLLGGGIWLISLGGSCYYLLCGAVMIACAILVFRHNKLALVIYA 64 Query: 69 LLLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGLYQPGKGALGAMGVALV 128 +LL + W VWEVG ++W L PR V + G L+LP + + + ++ + +L+ Sbjct: 65 ILLCFSTIWAVWEVGLNWWQLVPRLWVWFVMGWVLLLPPIRKTMMNNRLSSIMLL-TSLI 123 Query: 129 ASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRFSPLKQI 188 + V S+F P V+ G + T N +A P+ +A DW AY G +S L QI Sbjct: 124 VTTVVSVASLFTSPGVIEGKIENT--NLFRANPMQ-VAAEDWIAYGGTNAGLHYSALNQI 180 Query: 189 NHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAATGKQ 248 +N+ +LQ W+ +TGDM DP E+T+E TP+K+ D LY CT H + AL+ TGK Sbjct: 181 VPNNIHKLQEVWRIRTGDMPTADDPVELTNENTPLKVNDKLYTCTAHGWVLALEPETGKT 240 Query: 249 KWKFDPGLKTNP--TFQ---HVTCRGVSYHE-------FPAAKDASNTQPALCSRRIYLP 296 WKFDP + + TF+ H+TCRG+SY++ F K A + + C RRIYLP Sbjct: 241 LWKFDPAISNSGAGTFKGWAHMTCRGLSYYDSDRYLKQFAKDKIALKVKSSSCPRRIYLP 300 Query: 297 VNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVT 356 D RL AL+A+ G+ C +FG NG++DL TPG Y TSP ++T +++ G VT Sbjct: 301 TADARLIALNADNGQLCDSFGVNGQVDLTQGIGKFTPGGYYSTSPALVTKQLVIVGGHVT 360 Query: 357 DNFSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKL 416 DN ST EPSG +R FD+ G L+W +D G D + +T NSPN W+ D L Sbjct: 361 DNESTNEPSGVVRAFDIYDGHLVWNWDSGNPDATTPLPKDKKYTRNSPNVWSITSADEAL 420 Query: 417 DIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQP 476 +VYLP+G TPD +GGNRTP E+YA+ ++AL+ T+GK+VW+YQ HHDLWDMD+P+QP Sbjct: 421 GLVYLPLGNQTPDQYGGNRTPVVEKYAAGIVALDITSGKVVWNYQFTHHDLWDMDVPAQP 480 Query: 477 TLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSATQPY 536 L D+ G P + P K G+++VL+R+TG+ +VP E VPQGA KGD S TQ Sbjct: 481 ILVDLKTTQG-IEPAVIQPTKQGSLYVLNRKTGQPIVPINEVSVPQGAVKGDWTSPTQAR 539 Query: 537 SELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFEW 596 S+L P L ++DMWGAT +DQL CR+ FK LRYEG +TPPS QG+L++PGN+G+ W Sbjct: 540 SQLNLLPPP-LREQDMWGATPFDQLSCRIKFKSLRYEGQYTPPSLQGSLIYPGNVGVMNW 598 Query: 597 GGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPYGV 656 GG+++DP R+I A+P + F SKLIP+ E P A G G+QP G PY V Sbjct: 599 GGVAIDPVRKIIFASPNYMAFTSKLIPQA----EVPKNEANASEG--AGLQPNQGAPYAV 652 Query: 657 ELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSP-VPLPFKMGMPMLGG 715 + PFLS G PC+ P+WG V+ ++L N + W GT RD++P +PLPF +G+P +GG Sbjct: 653 RIQPFLSLVGFPCQAPSWGNVAGINLANNSIAWIHPNGTSRDNTPFIPLPFPVGVPAMGG 712 Query: 716 PVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTY-EVNGKQYVVIAAG 774 P+ TAG V F+ T D YLRA+ G+ +W +RLPAGGQATPMT+ + +QY+V+ G Sbjct: 713 PMTTAGGVAFLSGTLDQYLRAYDITNGKEIWSSRLPAGGQATPMTFWGKDNRQYIVLVVG 772 Query: 775 GHGSFGTKLGDYVIAYALPDQK 796 GHGSFGTK+GDY+IAYALP K Sbjct: 773 GHGSFGTKMGDYIIAYALPKNK 794 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: 2263 Number of extensions: 147 Number of successful extensions: 13 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: 803 Length adjustment: 41 Effective length of query: 755 Effective length of database: 762 Effective search space: 575310 Effective search space used: 575310 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