Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate Pf6N2E2_5442 Glucose dehydrogenase, PQQ-dependent (EC 1.1.5.2)
Query= CharProtDB::CH_002195 (796 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5442 Length = 804 Score = 774 bits (1998), Expect = 0.0 Identities = 393/810 (48%), Positives = 527/810 (65%), Gaps = 42/810 (5%) Query: 10 RLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALWLYA 69 RLL +L + L GL LL GG L +GGSWYY +AG+ + +L ++RAAL LYA Sbjct: 11 RLLPSLLGILLLLMGLALLAGGVKLSTLGGSWYYLLAGIGLALTGVLLIMARRAALGLYA 70 Query: 70 ALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGAVA--ALVVA 127 +L + +W +WEVG D+W L PR +L GI ++LP+ R L+ + A AL A Sbjct: 71 LVLFASTVWALWEVGLDWWQLVPRLALLFALGIVMLLPWFRRPLLTADASATGTRALGAA 130 Query: 128 LLISGGILTWAGFNDPQEINGTLSADATPAEAISPVA--DQDWPAYGRNQEGQRFSPLKQ 185 ++I+G + F +P EI G L D+ P A + A + DW +YGR+ G R+SPL Q Sbjct: 131 VVIAGVAALASQFTNPGEIKGQLDRDSVPGMANTAPAMPEGDWNSYGRSAHGDRYSPLAQ 190 Query: 186 INADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGK 245 I +NV L AW +RTGD+ PNDPGE T E TP+K LY+CT H ++ AL+ +GK Sbjct: 191 ITPENVSKLVPAWTYRTGDLPGPNDPGETTAENTPLKANGMLYVCTPHSQVIALEPETGK 250 Query: 246 EKWHYDPELKTNES-----FQHVTCRGVSYHE----AKAETASPEVMAD------CPRRI 290 E W +DP+L T ++ + H+TCRGV+YH+ A AE + V + CPRRI Sbjct: 251 EIWRFDPKLSTQKAENFKGWAHMTCRGVTYHDDAVYASAEQSPTGVASTSPASTTCPRRI 310 Query: 291 ILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAG 350 LP D RLIA+NA+ GK+CE F +KG ++L +N+ G Y TSPP +T +V+ G Sbjct: 311 FLPTADTRLIALNADTGKMCEDFGDKGQVDLTANIGGFTAGGYYSTSPPAVTQNLVVIGG 370 Query: 351 SVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYD 410 VTDN ST E SGVIR +DV+TG+L+W +D G D A ++ T+T NSPN W+ + D Sbjct: 371 HVTDNVSTDEPSGVIRAYDVHTGKLVWNWDSGNPDDTAPIAEGKTYTRNSPNMWSMFSVD 430 Query: 411 AKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLP 470 KL ++YLPMG TPD +GG RTPE E+YA+ + AL+ TGK+ W +Q HHDLWDMD+ Sbjct: 431 EKLGMLYLPMGNQTPDQFGGFRTPESEKYAAGLTALDIATGKVRWYFQFTHHDLWDMDVG 490 Query: 471 AQPTLADI-TVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPT 529 QPTL D+ T +G K P + A K G+I+VLDR NG+ ++P E PVPQGA +GD+ +PT Sbjct: 491 GQPTLMDMKTADGVK-PAVLASTKQGSIYVLDRSNGQPIIPIKEIPVPQGAVEGDHTSPT 549 Query: 530 QPFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGM 589 QP S+L+F P L DMWG T FDQ++CR+ F +RYEG+FTPPS QG++V+PGN G+ Sbjct: 550 QPMSDLNFVPPV-LKERDMWGVTPFDQMLCRIDFKSLRYEGMFTPPSLQGSIVYPGNFGV 608 Query: 590 FEWGGISVDPNREVAIANPMALPFVSKLIPR-----GPGNPMEQPKDAKGTGTESGIQPQ 644 F+WGGISVDP R++A NP + F SKL+P GPG E G+QP Sbjct: 609 FDWGGISVDPVRQIAFVNPSYMAFKSKLVPAAEVAGGPGRKSE----------TEGVQPN 658 Query: 645 YGVPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVP 704 G PYGV L LSP GLPC+ PAWGY++A+DL N+ +WK + GT +DS PVP+P Sbjct: 659 KGAPYGVILEALLSPMGLPCQAPAWGYVAAVDLTNNKTLWKHKNGTVRDS----SPVPIP 714 Query: 705 FNMGMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYE-VN 763 +MG+P LGG +TA + F++ T D YLRAY++ NG++LW+GRLPAG Q TPMTY + Sbjct: 715 LSMGVPSLGGTFTTASGLAFLSGTLDQYLRAYDVKNGKQLWEGRLPAGAQTTPMTYTGKD 774 Query: 764 GKQYVVISAGGHGSFGTKMGDYIVAYALPD 793 GKQYV++ AGGHGS GTK GDY++AY LPD Sbjct: 775 GKQYVLVVAGGHGSLGTKQGDYVIAYKLPD 804 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: 2243 Number of extensions: 148 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: 804 Length adjustment: 41 Effective length of query: 755 Effective length of database: 763 Effective search space: 576065 Effective search space used: 576065 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