Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate 3608903 Dshi_2294 Pyrrolo-quinoline quinone (RefSeq)
Query= CharProtDB::CH_002195 (796 letters) >FitnessBrowser__Dino:3608903 Length = 769 Score = 560 bits (1444), Expect = e-164 Identities = 307/791 (38%), Positives = 448/791 (56%), Gaps = 33/791 (4%) Query: 15 LTALFAA---LCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALWLYAAL 71 +T LF A L G + + G WL+A+GGSWYY +AG + + W+ + W++ A+ Sbjct: 1 MTKLFGAILVLVGALMFVPGIWLIALGGSWYYSLAGAGLAAAGFYYWKKQLLGAWIFGAV 60 Query: 72 LLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGAVAALVVALLIS 131 GT +W VWEVGF+ W L PR LV + IL + + G A+L A +++ Sbjct: 61 FAGTALWAVWEVGFELWPLVPR---LVAPMVLAILAVLLVPSLNEGRGRTASLAAAGVLA 117 Query: 132 GGILTWA-GFNDPQEINGTLSADATPAEAISPVADQDWPAYGRNQEGQRFSPLKQINADN 190 GI + G PQ + + D P AI+ +W YGR G RF+P QI +N Sbjct: 118 LGIAGFFWGMATPQNV--IANTDPVPTRAIA-AESPNWTHYGRTPTGTRFAPFDQITPEN 174 Query: 191 VHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGKEKWHY 250 V L+ AW F GD P+ G+ N TP+ V +Y C+ + + A+DA +G + W Y Sbjct: 175 VGELEVAWTFNHGDA--PSGTGQDQN--TPLYVDGLVYHCSPNNIVSAIDAVTGAQVWQY 230 Query: 251 DPELKTNESFQHVTCRGVSYHEAKAETASPEVMADCPRRIILPVNDGRLIAINAENGKLC 310 DPE ++ +Q CRGV+Y+E +P C RI+L D RLI ++A G LC Sbjct: 231 DPEA-SSPLWQR--CRGVTYYEPTPREGAP-ADGTCAARIVLSSVDARLIQLDARTGALC 286 Query: 311 ETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSVTDNFSTRETSGVIRGFDV 370 TF + G ++L NM + +PG Y PTS P + I++ G V D + E SGV+R FD Sbjct: 287 TTFGDGGAVDLTRNMGEVRPGFYFPTSAPTVMGDRIILGGWVWDGMAVDEPSGVVRAFDG 346 Query: 371 NTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKLDLVYLPMGVTTPDIWGG 430 TGE+ WA+D G + +P + T+T +PN W+ A+DA L LVYLP G PD +G Sbjct: 347 RTGEIAWAWDIGNPAIDTVPPEGETYTRGTPNVWSTPAFDAALGLVYLPTGNAQPDFYGS 406 Query: 431 NRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPAQPTLADITV-NGQKVPVIY 489 +R + SSI+AL+ TGK+ WS+QT + D+WD D+PAQP L DIT G+ VP + Sbjct: 407 SRIEAANDWNSSIVALDVETGKVVWSFQTTYRDIWDYDVPAQPMLYDITTETGEVVPALI 466 Query: 490 APAKTGNIFVLDRRNGELVVPAPEKPVP-QGAAKGDYVTPTQPFS-ELSFRPTKDLSGAD 547 K FVLDRR+G + + PVP G + DY++P QP+S ++ + L+ A Sbjct: 467 QVTKRSQTFVLDRRDGTPIAEVRDLPVPTTGGVEPDYLSPVQPYSVDMPVIGAEPLTEAR 526 Query: 548 MWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGMFEWGGISVDPNREVAIAN 607 MWGAT D L CR+ F Q Y G FTP SEQGTL++PG G WG ++D R + I N Sbjct: 527 MWGATPLDHLYCRIRFRQAYYVGDFTPMSEQGTLIWPGYFGGMNWGTGTIDEARGLLIVN 586 Query: 608 PMALPFVSKLIPRGPGNPMEQPKDAKG---TGTESGIQPQYGVPYGVTLNPFLSPFGLPC 664 + + +LIPR Q DA G G G+ PQ G P+G + F S G+PC Sbjct: 587 DTRVAHLLQLIPR-------QEADALGVEVVGPHDGLAPQDGAPFGAMRSNFFSFVGVPC 639 Query: 665 KQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLGGPISTAGNVLF 724 ++P +G ++A+DL ++W++ +GT +++ PF + +G+P++GGPISTA + F Sbjct: 640 QEPPYGTMTAIDLADRSILWQRPVGTIEETGPFGIRTGWRMPVGLPLVGGPISTASGLTF 699 Query: 725 IAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTY-EVNGKQYVVISAGGHGSFGTKMG 783 + T D YLRA++ GE+LW+G LP G Q+TPM+Y +G+QYVV++ GG + G Sbjct: 700 YSGTQDYYLRAFSSETGEELWRGALPLGSQSTPMSYIGPDGRQYVVVTVGGLNDIMGR-G 758 Query: 784 DYIVAYALPDD 794 D ++A+ALP++ Sbjct: 759 DIVMAFALPEE 769 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: 2286 Number of extensions: 169 Number of successful extensions: 15 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 796 Length of database: 769 Length adjustment: 41 Effective length of query: 755 Effective length of database: 728 Effective search space: 549640 Effective search space used: 549640 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