Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate H281DRAFT_03298 H281DRAFT_03298 quinoprotein glucose dehydrogenase
Query= BRENDA::D4P700 (796 letters) >FitnessBrowser__Burk376:H281DRAFT_03298 Length = 879 Score = 578 bits (1490), Expect = e-169 Identities = 281/509 (55%), Positives = 352/509 (69%), Gaps = 9/509 (1%) Query: 287 ALCSRRIYLPVNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITD 346 A C RRI+LP D RL AL+A+TG+ C FGNNG++DL+ TPG Y TSPP +T Sbjct: 378 AECPRRIFLPTADARLIALNADTGQPCTHFGNNGQIDLRTNIGPFTPGGYYSTSPPAVTR 437 Query: 347 TTIVMAGAVTDNFSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNS 406 ++++G VTDN ST EPSG R FDV+ G L+W +D G D T+ NSPN Sbjct: 438 DLVIISGHVTDNESTNEPSGVTRAFDVHDGHLVWNWDAGNPDETQPITGNQTYVRNSPNM 497 Query: 407 WAPAVYDPKLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHD 466 W+ D KL +VYLP+G TPD WGG RTP E+ A+ V+AL+ TGK+ W+YQ HHD Sbjct: 498 WSVFSVDEKLGMVYLPLGNQTPDQWGGMRTPASEKVAAGVVALDLATGKMRWNYQFTHHD 557 Query: 467 LWDMDLPSQPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAK 526 LWDMD+ QP+L D+ G P + A K G+++VL+R TGK +VP E PVPQGA Sbjct: 558 LWDMDVGGQPSLIDLQTPSG-VQPALIASTKQGSLYVLNRETGKPIVPITEEPVPQGAGT 616 Query: 527 GDHVSATQPYSELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLV 586 GDH S TQP+S L F+P + + ++DMWG +DQL CRV FK LRY+G FTPPSEQG+LV Sbjct: 617 GDHTSPTQPFSALNFKPPK-VRERDMWGTNPFDQLWCRVKFKSLRYDGMFTPPSEQGSLV 675 Query: 587 FPGNLGMFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTET-G 645 FPGN G+F+WGGI+VDP RQI IANP + F SKL+PR + P G+ET G Sbjct: 676 FPGNFGVFDWGGIAVDPVRQILIANPSYMAFTSKLVPR-----SQIPSDNGEKKGSETSG 730 Query: 646 IQPQYGVPYGVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLP 705 I+ G PYG ELN FLSP G+PC+ P WGYV+ VDL+TN +VW+ + GT+RDS+P+P+P Sbjct: 731 IKLARGTPYGFELNAFLSPLGIPCQAPPWGYVAGVDLRTNHIVWEHKNGTIRDSAPLPIP 790 Query: 706 FKMGMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTY-EVN 764 +G+P LGG + TAG V F+ T D YLRA+ TG+ LWQARLPAGGQATPMTY + N Sbjct: 791 MPLGVPSLGGMITTAGGVAFLSGTLDYYLRAYDVRTGDRLWQARLPAGGQATPMTYADSN 850 Query: 765 GKQYVVIAAGGHGSFGTKLGDYVIAYALP 793 GKQYV++ AGGHGS GTK GDYVIAY LP Sbjct: 851 GKQYVLVTAGGHGSLGTKQGDYVIAYTLP 879 Score = 208 bits (529), Expect = 1e-57 Identities = 114/266 (42%), Positives = 158/266 (59%), Gaps = 14/266 (5%) Query: 20 VLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYALLLLATLAWGV 79 ++ G + GG+ L +GGSWYY++ G A+ LT LL R +AL ++AL+L + W V Sbjct: 19 IIIGLALAGGGVPLVALGGSWYYVVTGIAIALTGVLLSIRRRSALWLFALILFGSTIWAV 78 Query: 80 WEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGLYQPGKGALGAMGVALVASAAVLTY--- 136 E DFW L PR V ++ +WL+LP V R L G A GV + +A +LT Sbjct: 79 VEARFDFWQLLPRLWVWLVLALWLLLPPVTRKLVF-GPPAAHREGVVPLTAAVILTVLLG 137 Query: 137 --SVFNDPQVVNGALPATADNAPQAQPLSNIAD---GDWPAYARDQQGTRFSPLKQINHD 191 + FN P G L +TA AP P++ A+ DW Y G R+SPL QI + Sbjct: 138 LVTAFNHPYDRAGTLASTA--APPTTPIAGDANRQAADWTDYGGSPLGQRYSPLTQITPE 195 Query: 192 NVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAATGKQKWK 251 N +L+VAWQF+TGD P DP E TDE TPIK+ + L+LCTPH I+ ALD A+GK+ W+ Sbjct: 196 NAGQLKVAWQFETGDKPGPGDPTETTDENTPIKVGNKLFLCTPHSIVIALDPASGKELWR 255 Query: 252 FDPGLKTNPTF---QHVTCRGVSYHE 274 +DP +++ F +H+TCRGVSYH+ Sbjct: 256 YDPHIQSPVGFKHWEHMTCRGVSYHD 281 Score = 28.5 bits (62), Expect = 0.002 Identities = 23/75 (30%), Positives = 31/75 (41%), Gaps = 16/75 (21%) Query: 240 ALDAATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKD---ASNTQPALCSRRIYLP 296 ALD ATGK +W + F H + P+ D S QPAL + Sbjct: 539 ALDLATGKMRWNYQ--------FTHHDLWDMDVGGQPSLIDLQTPSGVQPALIA-----S 585 Query: 297 VNDGRLFALDAETGE 311 G L+ L+ ETG+ Sbjct: 586 TKQGSLYVLNRETGK 600 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: 2638 Number of extensions: 190 Number of successful extensions: 13 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 6 Number of HSP's successfully gapped: 3 Length of query: 796 Length of database: 879 Length adjustment: 42 Effective length of query: 754 Effective length of database: 837 Effective search space: 631098 Effective search space used: 631098 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: 56 (26.2 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