Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate N515DRAFT_0461 N515DRAFT_0461 quinoprotein glucose dehydrogenase
Query= CharProtDB::CH_002195 (796 letters) >FitnessBrowser__Dyella79:N515DRAFT_0461 Length = 816 Score = 795 bits (2054), Expect = 0.0 Identities = 404/814 (49%), Positives = 531/814 (65%), Gaps = 48/814 (5%) Query: 15 LTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALWLYAALLLG 74 +TA GL LL GG WL+ +GGS YY +AG +++ W+ WR AL L+A LLL Sbjct: 13 ITAALFVFLGLGLLAGGAWLLVLGGSPYYVLAGAMLIATGWLAWRGSGLALGLHALLLLA 72 Query: 75 TMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIP-------ASGAVAA-LVV 126 T++W ++EV FD+W L PR + G+WL+LP+V RRL A+G + LV+ Sbjct: 73 TLLWAIYEVRFDWWQLVPRVAVWFVLGVWLLLPWVSRRLEPDPEPTLRWATGTLPLWLVL 132 Query: 127 ALLISGGILTWAGFNDPQEINGTL-SADATPAEAISPVADQDWPAYGRNQEGQRFSPLKQ 185 A ++ G + + F D + G A A PA+A DW AYGR+ G R +P Q Sbjct: 133 AASVALGAVAY--FTDYYTLAGEAPEAGAPPADATG-TPPNDWIAYGRSGHGDRHAPAAQ 189 Query: 186 INADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGK 245 I NV L+ AW F TGD K P DP EI NEVTP+K LYLCT H + ALD +GK Sbjct: 190 ITPANVAKLQVAWTFHTGDFKGPGDPTEIANEVTPLKANGMLYLCTPHDIVIALDPDTGK 249 Query: 246 EKWHYDPELKTN-ESFQHVTCRGVSYHE-----AKAETASPEVMA--------------- 284 E+W YDP++ + + +QH+ CRGV+YH+ A+A TA A Sbjct: 250 ERWRYDPKINRDAKGYQHMICRGVAYHDSGAYAAQAATAGVAPAAPPPTPKGAVAAEAIH 309 Query: 285 --DCPRRIILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIIT 342 CPRRI P D ++A+NA+NG+ C F + GV+ L M + G PTSPP +T Sbjct: 310 FDSCPRRIFAPTADATVVALNADNGQPCTDFGDHGVIGLYQGMAMKRRGFLNPTSPPTVT 369 Query: 343 DKTIVMAGSVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNA-IPSDEHTFTFNSP 401 ++++ SVTDN ST E SGVIRG+DV TG+LLW +D A D A +P+ +H + NSP Sbjct: 370 RNVLIVSASVTDNESTDEPSGVIRGYDVTTGQLLWNWDAAAPDSTAPLPAGQH-YKRNSP 428 Query: 402 NSWAPAAYDAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVH 461 NSW+ ++ D KL LVY+PMG TPD+WGG R PE ER+ S+I+AL+ TGKL W YQTVH Sbjct: 429 NSWSVSSVDEKLGLVYIPMGNQTPDMWGGERYPEGERFNSAIVALDIATGKLRWVYQTVH 488 Query: 462 HDLWDMDLPAQPTLADITVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAA 521 HDLWDMD+ QP+L D+ KVP + A K G+I+VLDRR+G+ VVPAPE+PVPQGAA Sbjct: 489 HDLWDMDIGGQPSLVDLDTPQGKVPALVASTKRGDIYVLDRRDGKPVVPAPERPVPQGAA 548 Query: 522 KGDYVTPTQPFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTL 581 GD +PTQPFS LSF P L ADMWG +DQLVCR+ F ++RY+GIFTPPSEQG+L Sbjct: 549 TGDRTSPTQPFSALSFAPEHPLREADMWGTNPYDQLVCRIKFRRLRYDGIFTPPSEQGSL 608 Query: 582 VFPGNLGMFEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKG-TGTESG 640 V+PGN G+F+WGG++VDP R++ I NP + F+S+LI R E+ + AKG TG E G Sbjct: 609 VYPGNYGVFDWGGVTVDPQRQLLIGNPNYMAFMSRLITR----ETEEARSAKGSTGIEHG 664 Query: 641 IQPQYGVPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMP 700 +QP G P+ V L P LSP G+PC+ P WGY++A+DL+T +W R GT DS P P+P Sbjct: 665 LQPMQGTPFAVDLRPLLSPLGIPCQAPPWGYVAAVDLRTMRKLWMHRNGTVVDSAPLPIP 724 Query: 701 VPVPFNMGMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTY 760 +P +G+P LGG I+T G V F++A+ D YLRAY++ NG++LW+ RLPAGGQATPM+Y Sbjct: 725 LP----LGVPSLGGMITTGGGVAFMSASLDYYLRAYDVRNGKQLWEARLPAGGQATPMSY 780 Query: 761 --EVNGKQYVVISAGGHGSFGTKMGDYIVAYALP 792 + G+QYVVI AGGHGS GTKMGD ++AYALP Sbjct: 781 VSDQTGRQYVVIMAGGHGSLGTKMGDALIAYALP 814 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: 2448 Number of extensions: 137 Number of successful extensions: 12 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: 816 Length adjustment: 41 Effective length of query: 755 Effective length of database: 775 Effective search space: 585125 Effective search space used: 585125 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