Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate BWI76_RS16705 BWI76_RS16705 glucose dehydrogenase
Query= BRENDA::D4P700 (796 letters) >FitnessBrowser__Koxy:BWI76_RS16705 Length = 801 Score = 553 bits (1425), Expect = e-161 Identities = 321/807 (39%), Positives = 451/807 (55%), Gaps = 38/807 (4%) Query: 8 FSVVRFLTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVY 67 F+V R L VL + G F + G L ++GGS +Y++ G A LL A R+ L Sbjct: 13 FTVYRLLFVLLSFGIGLFFTLWGGKLLSLGGSAWYLLAGLAYLLIAVGYLIRSRYVLPFA 72 Query: 68 ALLLLATLAWGVWEVGTDFWALAPRTDV---LVIFGVWLVLPFVYRGLYQPGKGALGAMG 124 L L TL W ++EV +W L PR V +++ +WL R + + A + Sbjct: 73 ILTFLLTLCWALYEVQFSYWGLIPRLVVPALMLMLALWLAATLPMRPARR--RYANWSAS 130 Query: 125 VALVASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRFSP 184 + A L + + + NG + A+ D P S+ +W + RD GTRF+P Sbjct: 131 AIFLVLLATLVSAFYPHGAIHNGVVNASGDATPTLASKSD----NWAFFGRDASGTRFAP 186 Query: 185 LKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAA 244 +I NVK L+VAW + TG +R + G DE TP++I DTLY CTP ++ ALDA Sbjct: 187 YDEITPQNVKNLKVAWTYHTG--RRLTGAGIGVDENTPLQIGDTLYSCTPLNVVTALDAD 244 Query: 245 TGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDAS---NTQPAL--CSRRIYLPVND 299 TGK +W+FDP T +HVTCRGV Y++ + S PAL C +RI + D Sbjct: 245 TGKARWRFDPHAGTA---EHVTCRGVGYYDVQSDDSLSAEEKASPALLQCPQRILVSTVD 301 Query: 300 GRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGM-YEPTSPPVITDTTIVMAGAVTDN 358 RL AL+A+TGE C FG++G +DL+ T Y PTS PVI V+ G V D Sbjct: 302 ARLIALNAKTGEPCDDFGDHGSVDLKQGMDNTENSKRYHPTSTPVIMGHIAVLGGWVRD- 360 Query: 359 FSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDI 418 EPSG +R FDV G ++W +D G + P +T+ +PN W +D +L++ Sbjct: 361 IVHGEPSGVVRAFDVRNGNVVWAWDVGQPENVTDPVKGRVYTLETPNVWTVPGFDKELNL 420 Query: 419 VYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTL 478 +YLP G PD WGG+R +E+Y SSV+A++A+TG+ W +QTVHHD+WD DLPSQP L Sbjct: 421 IYLPTGNGPPDYWGGDRNAAKEKYGSSVVAVDASTGETKWVFQTVHHDIWDYDLPSQPVL 480 Query: 479 ADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSATQPYSE 538 + ++ G VPV+ KTG I+VLDRRTGK V E PV A+G+H+SATQP+S Sbjct: 481 FHMKNERGEEVPVLIQTTKTGQIYVLDRRTGKPVTRVEERPVAHDGAEGEHLSATQPFS- 539 Query: 539 LTFRPK---QNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFE 595 T P+ + LT+K MWG T +DQL+CR+ FK Y G +TPPSE+ + +P LG Sbjct: 540 -TGMPQLGVEPLTEKSMWGVTPFDQLMCRIDFKESTYLGMYTPPSEKPYIEWPSLLGGMN 598 Query: 596 WGGISVDPHRQIAIANPMALPFVSKLIPR-GPGNPEEPPKGATGGSGTETGIQPQYGVPY 654 WGGI++D N M +P L+ + + G GT ++PQ PY Sbjct: 599 WGGITIDERTGTLFVNDMRMPLRMSLVRKEDMAKYKVSTDEVPGFMGT---VRPQIAGPY 655 Query: 655 -GVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLPFKM----G 709 GV ++ S G+PC P +G +SA+DL T +++W+ +G+V D+ P+ L M G Sbjct: 656 GGVRIDILQSALGVPCNTPPFGTMSAIDLNTRQLMWQVPMGSVEDTGPLGLKTHMHIPLG 715 Query: 710 MPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTYE--VNGKQ 767 MP LGGP +TA + F T DNYLRA + TG+ LW+ARLP G A P+ Y+ GK+ Sbjct: 716 MPTLGGPTSTASGLVFFAGTQDNYLRALDSATGKELWRARLPVGAVAAPLIYKSPKTGKE 775 Query: 768 YVVIAAGGHGSFGTKLGDYVIAYALPD 794 YVVI+AGG S +GD +IA+AL + Sbjct: 776 YVVISAGG-ASHSPDVGDDIIAFALEE 801 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: 2190 Number of extensions: 140 Number of successful extensions: 16 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: 801 Length adjustment: 41 Effective length of query: 755 Effective length of database: 760 Effective search space: 573800 Effective search space used: 573800 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