Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate GFF1045 PS417_05300 glucose dehydrogenase
Query= CharProtDB::CH_002195 (796 letters) >FitnessBrowser__WCS417:GFF1045 Length = 805 Score = 755 bits (1949), Expect = 0.0 Identities = 386/805 (47%), Positives = 516/805 (64%), Gaps = 31/805 (3%) Query: 10 RLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALWLYA 69 RLL L + + GL LL GG L +GGS YY +AG+ + +L ++RAAL LYA Sbjct: 11 RLLPRLLGVLLLIMGLALLAGGIKLTMLGGSLYYLLAGIGITLTGVLLLATRRAALGLYA 70 Query: 70 ALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVI--PASGAVAALVVA 127 +L + +W +WEVG D+W L PR +L GI ++LP+ R L+ PA AL VA Sbjct: 71 LVLFASTVWALWEVGLDWWQLVPRLALLFALGIVMLLPWFRRPLLRGQPAPLGTGALSVA 130 Query: 128 LLISGGILTWAGFNDPQEI--NGTLSADATP--AEAISPVADQDWPAYGRNQEGQRFSPL 183 ++++G + F +P E+ G L DA P A A A+ DW +YGR+ G R+SPL Sbjct: 131 VVLAGATALASQFTNPGEMVKTGQLDRDAVPGMASAAPSQAEGDWNSYGRSAYGDRYSPL 190 Query: 184 KQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAAS 243 QI +N H L AW +RTGD+ PNDPGE T E TP+KV LY+CT H ++ ALD + Sbjct: 191 AQITPENAHKLVPAWTYRTGDIPGPNDPGETTAENTPLKVNGMLYVCTPHSQVIALDPDT 250 Query: 244 GKEKWHYDPELKTN--ESFQ---HVTCRGVSYHEAKAE--------TASPEVMAD-CPRR 289 GKE W +DP++ + E+F+ H+TCRGVSYH+ A +ASP + CP+R Sbjct: 251 GKEIWRFDPKISSMGAENFKGWAHMTCRGVSYHDDAAYASEQSPTGSASPSAAPNACPKR 310 Query: 290 IILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMA 349 I +P D RLIA+NA+ GK+CE F +KG ++L++N+ PG Y TSPP +T +V+ Sbjct: 311 IFVPTADTRLIALNADTGKMCEDFGDKGQVDLRANIGGFAPGGYYSTSPPAVTKNLVVIG 370 Query: 350 GSVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAY 409 G VTDN ST E SGVIR FDV+TG+L+W +D G D ++ T+T NSPN W+ A Sbjct: 371 GHVTDNVSTDEPSGVIRAFDVHTGKLVWNWDSGNPDDTTPLAEGKTYTRNSPNMWSMFAV 430 Query: 410 DAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDL 469 D KL ++YLPMG PD +GG+RT + E+YA+ + AL+ TG + W++Q HHDLWDMD+ Sbjct: 431 DEKLGMLYLPMGNQMPDQYGGDRTDDSEKYAAGLTALDIDTGHVKWTFQFTHHDLWDMDV 490 Query: 470 PAQPTLADITVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPT 529 QP+L DI + A K G+I+VLDR G+ VVP E VPQGA GD +PT Sbjct: 491 GGQPSLIDIKTEAGVKQAVMASTKQGSIYVLDRATGQPVVPIHEVAVPQGAVAGDRTSPT 550 Query: 530 QPFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGM 589 QP S+L+F P L DMWG T FDQL+CR+ F MRY+G FTPPS QG++V+PGN G+ Sbjct: 551 QPKSDLNFMP-PPLKERDMWGVTPFDQLLCRIDFKSMRYDGAFTPPSLQGSIVYPGNFGV 609 Query: 590 FEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGVPY 649 F+WGGISVDP R++A NP + F SKLIP + K G+QP G PY Sbjct: 610 FDWGGISVDPVRQIAFVNPSYMAFKSKLIPAA-----DIAKQGPRVSETEGVQPNKGAPY 664 Query: 650 GVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGM 709 GV L LSP GLPC+ PAWGY++A+DL T++ +W + GT +DS PVP+P MG+ Sbjct: 665 GVILEAMLSPMGLPCQAPAWGYVAAVDLTTHKTIWMHKNGTVRDS----APVPIPLTMGV 720 Query: 710 PMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYE-VNGKQYV 768 P LGG +TAG V F++ T D YLRAY++ NG++LW+GRLPAG Q TPMTY +GKQYV Sbjct: 721 PSLGGTFTTAGGVAFLSGTLDQYLRAYDVKNGKQLWEGRLPAGAQTTPMTYTGKDGKQYV 780 Query: 769 VISAGGHGSFGTKMGDYIVAYALPD 793 ++ AGGHGS GTK GDY++A+ LP+ Sbjct: 781 LVMAGGHGSLGTKQGDYVMAFKLPE 805 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: 2240 Number of extensions: 152 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: 805 Length adjustment: 41 Effective length of query: 755 Effective length of database: 764 Effective search space: 576820 Effective search space used: 576820 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