Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate GFF2858 Psest_2914 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family
Query= BRENDA::D4P700 (796 letters) >FitnessBrowser__psRCH2:GFF2858 Length = 776 Score = 782 bits (2020), Expect = 0.0 Identities = 386/784 (49%), Positives = 509/784 (64%), Gaps = 23/784 (2%) Query: 17 LFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYALLLLATLA 76 LF ++ G + +GG + ++GG+WY+ I A LLT LL R AL VYALL+L L Sbjct: 8 LFCIIVGIALGVGGAKVVSLGGTWYFAIVAAGFLLTGVLLLMRRRTALWVYALLMLGALG 67 Query: 77 WGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGL------YQPGKGALGAMGVALVAS 130 W V+EVG D+W LAPR ++ FG+WL+ P++ R L ++ GA + +A+ Sbjct: 68 WAVYEVGLDWWQLAPRGSIIAPFGLWLLTPWIARRLGWQHFGFRAWGGAALPLMLAVGLW 127 Query: 131 AAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRFSPLKQINH 190 A Y+V +D + G LPA AP A ++ GDW AY R Q G R+SPL QI Sbjct: 128 GAATVYAVGHDGHDIKGMLPAPLAQAPAAD--DSVPAGDWHAYGRSQHGQRYSPLAQITP 185 Query: 191 DNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAATGKQKW 250 NV L+ W +QTGD++ P DP E T EVTP+K+ D+LYLCTPH ++ ALDA TG+++W Sbjct: 186 QNVDRLEPVWHYQTGDLRGPDDPDETTYEVTPLKVDDSLYLCTPHNLVIALDAETGQERW 245 Query: 251 KFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVNDGRLFALDAETG 310 +FDP + + QH+TCRG+SYH P D C +R+++P D RL ALDA+TG Sbjct: 246 RFDPKVPHSVNRQHLTCRGLSYHAAPQGSDVQ-----ACRQRLFMPTADARLIALDAKTG 300 Query: 311 ERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDNFSTREPSGAIRG 370 E CP F +NGE+DL P G Y TSPPV+ +++ GAV DN +EPSG IR Sbjct: 301 EICPGFADNGEIDLWANMPHAKEGFYYSTSPPVVARDLVIIGGAVNDNVRAQEPSGVIRA 360 Query: 371 FDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDIVYLPMGVTTPDI 430 +DV TG+L W +DPG D A T++ +SPNSW+ + D L +VY+P+G PD Sbjct: 361 YDVYTGQLKWNWDPGNPDATEPIAAGQTYSPSSPNSWSISSADEALGMVYVPLGNQVPDQ 420 Query: 431 WGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTLADITDKDGNTVP 490 WGG R ER++SS++AL+ +G+L W +QTV HDLWDMD+P+QP+L DI ++G VP Sbjct: 421 WGGRRNENSERFSSSIVALDLDSGQLRWVFQTVRHDLWDMDVPAQPSLVDIQTENG-PVP 479 Query: 491 VIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSATQPYSELTFRPKQNLTDK 550 + AP K G+I+VLDRRTG+ ++P E P PQGAA+GD V+ TQP S L++ P + L K Sbjct: 480 AVVAPTKQGDIYVLDRRTGEPILPVREVPAPQGAAEGDWVAKTQPASALSYEPPK-LQGK 538 Query: 551 DMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFEWGGISVDPHRQIAIA 610 D+WGAT+ DQ++C + F LRYEG +TPPS QGTLV PGN G+F WGG++VDP RQ+ + Sbjct: 539 DLWGATLIDQMMCHIQFHSLRYEGRYTPPSTQGTLVHPGNFGVFNWGGVAVDPVRQMVFS 598 Query: 611 NPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPYGVELNPFLSPFGLPCK 670 P L F SKLIPR T S E + +G P+ VEL F+SP GLPC Sbjct: 599 TPAYLAFTSKLIPREDAE-------TTYVSEQEPFLNENFGSPFAVELKAFVSPIGLPCT 651 Query: 671 QPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLPFKMGMPMLGGPVATAGKVFFIGATA 730 P WGYV+ DL+T + W ++ GTVRD SP+PLPFKMG+P LGGP+ TAG V F+ T Sbjct: 652 APPWGYVAGADLRTGKTHWLRKNGTVRDRSPIPLPFKMGVPNLGGPMLTAGGVAFLSGTL 711 Query: 731 DNYLRAFSTDTGELLWQARLPAGGQATPMTYEV-NGKQYVVIAAGGHGSFGTKLGDYVIA 789 D YLRA+ TG LW+ARLPAGGQATPMTY+ +G+Q VV+ AGGHGS GTK GD VIA Sbjct: 712 DYYLRAYDVMTGRELWKARLPAGGQATPMTYQSRSGRQMVVVVAGGHGSLGTKAGDSVIA 771 Query: 790 YALP 793 YALP Sbjct: 772 YALP 775 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: 2264 Number of extensions: 151 Number of successful extensions: 14 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: 776 Length adjustment: 41 Effective length of query: 755 Effective length of database: 735 Effective search space: 554925 Effective search space used: 554925 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 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