Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate BWI76_RS13270 BWI76_RS13270 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family
Query= CharProtDB::CH_002195 (796 letters) >FitnessBrowser__Koxy:BWI76_RS13270 Length = 790 Score = 641 bits (1653), Expect = 0.0 Identities = 341/810 (42%), Positives = 491/810 (60%), Gaps = 39/810 (4%) Query: 1 MAINNT--GSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLW 58 MA +N G R+L L A + GL + I G L ++GG++Y+ + GLVM+ A +++ Sbjct: 1 MATDNAPRGFPRILQWLLAGLMLIIGLAIGILGAKLASVGGTFYFALMGLVMVIAAVLIF 60 Query: 59 RSKRAALWLYAALLLGTMIWGVWEVGFDFWALTPRSDIL--VFFGIWLILPFVWRRLVI- 115 RS+R + LYA + +++W + + G+ +W L R L + F L+ PF+ R+ Sbjct: 61 RSRRGGIMLYAVAFVASIVWAISDAGWTYWPLFSRLFALGVLAFLCALVWPFLSRQPAKK 120 Query: 116 -PASGAVAALVVALLISGGILTWAGFNDPQEINGTLSADATPAEAISPVA----DQDWPA 170 PA G A + VALL+S W + P A+ A + PVA ++W Sbjct: 121 GPAFGLAAVIAVALLVS---FAWMFKSQPL-------VSASEAVPVKPVAADEQQKNWAH 170 Query: 171 YGRNQEGQRFSPLKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLC 230 +G G RF+ L QIN NV L+ AW+ TGD+ Q N G ++ TP+++GDTLY+C Sbjct: 171 WGNTTHGDRFAALDQINKQNVDQLQVAWIAHTGDIPQSNGSGA-EDQNTPLQIGDTLYVC 229 Query: 231 TAHQRLFALDAASGKEKWHYDPELKTNESFQHVTCRGVSYHEAKAETASPEVMAD---CP 287 T + ++ ALD SGKEKW YD + T ++Q CRG+ Y+E SP A C Sbjct: 230 TPYSKVLALDVDSGKEKWRYDSKA-TAPNWQR--CRGLGYYEDSQAQVSPAADAQPAACS 286 Query: 288 RRIILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIV 347 RR+ LP D RLIAI+A+NGKLC+ F + G+++L M + K G Y+ TS P++ +V Sbjct: 287 RRLFLPTTDARLIAIDADNGKLCDAFGDHGIVDLSIGMGEIKAGYYQQTSTPLVAGNVVV 346 Query: 348 MAGSVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPA 407 + G V DNFST E GV+R +DV+TG+L WA+DPG P T+T +PN W+ Sbjct: 347 VGGRVADNFSTGEPPGVVRAYDVHTGKLAWAWDPGNPALTGEPPAGQTYTRGTPNVWSAM 406 Query: 408 AYDAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDM 467 +YDAKL+L+YLP G TPD +GG RT ++Y+SSI+A++ATTG++ W YQT HHDLWD Sbjct: 407 SYDAKLNLIYLPTGNATPDFFGGERTALDDKYSSSIVAVDATTGQVRWHYQTTHHDLWDF 466 Query: 468 DLPAQPTLADI-TVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYV 526 DLP+QP L D+ G PV+ +K G IF+L+R GE V E+PVP G KG+ Sbjct: 467 DLPSQPLLYDLPDGKGGTTPVLVQTSKQGMIFMLNRATGEPVAKVEERPVPAGNVKGERY 526 Query: 527 TPTQPFS-ELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPG 585 +PTQP+S + + L+ +DMWGAT D L+CR+ F +MR++G+FTPP E +L +PG Sbjct: 527 SPTQPYSVGMPMIGNETLTESDMWGATPVDLLLCRIQFKEMRHQGVFTPPGEDRSLQYPG 586 Query: 586 NLGMFEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQY 645 +LG WG +SVDPN + N M L + ++PR + KDA +G E GI P Sbjct: 587 SLGGMNWGSVSVDPNNSLIFVNDMRLGLANYMVPRA-----KVAKDA--SGIEMGIVPME 639 Query: 646 GVPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPF 705 G P+G FLSP G+PC++P +G +SA+DLKT ++VW+ +GT +D+ P + + +P Sbjct: 640 GTPFGAMRERFLSPLGIPCQKPPFGTLSAVDLKTGKLVWQVPVGTVEDTGPLGIRMHMPI 699 Query: 706 NMGMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTY--EVN 763 +GMP LG +ST +LF A T D YLRA++ +NG+++W+ RLP G Q+ PMTY Sbjct: 700 PIGMPTLGASLSTQSGLLFFAGTQDFYLRAFDTANGKEIWKSRLPVGSQSGPMTYVSPKT 759 Query: 764 GKQYVVISAGGHGSFGTKMGDYIVAYALPD 793 GKQY++I+AGG GDYI+AYALP+ Sbjct: 760 GKQYIIINAGG-ARQSPDRGDYIIAYALPE 788 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: 2187 Number of extensions: 139 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: 790 Length adjustment: 41 Effective length of query: 755 Effective length of database: 749 Effective search space: 565495 Effective search space used: 565495 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