Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate PfGW456L13_4805 Glucose dehydrogenase, PQQ-dependent (EC 1.1.5.2)
Query= CharProtDB::CH_002195 (796 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4805 Length = 803 Score = 748 bits (1930), Expect = 0.0 Identities = 378/807 (46%), Positives = 532/807 (65%), Gaps = 37/807 (4%) Query: 10 RLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALWLYA 69 RLL TL + L GL +L GG L +GGS YY +AG+ + +L ++RAAL LYA Sbjct: 11 RLLPTLLGILLLLMGLAMLAGGIKLSMLGGSLYYLLAGIGIALSGVLLIAARRAALGLYA 70 Query: 70 ALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVI--PASGAVAALVVA 127 +L + +W +WEVG D+W L PR + G+ ++LP+ R L+I PA AL VA Sbjct: 71 LVLFASTVWALWEVGLDWWQLVPRLALWFALGVVMLLPWFRRPLLINGPAPMGTGALSVA 130 Query: 128 LLISGGILTWAGFNDPQEINGTLSADATPAEAISP-VADQDWPAYGRNQEGQRFSPLKQI 186 ++++G + F P E G L D + +P + + DW AYGR++ G R+SPLKQI Sbjct: 131 VVLAGATAVASQFTHPGETFGELGRDTADMTSTAPQMPEGDWQAYGRSEFGDRYSPLKQI 190 Query: 187 NADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGKE 246 NV L+EAW +TGD+ +DP E+TNE TP+K LY CTAH ++ ALD +GKE Sbjct: 191 TPANVGKLQEAWRIQTGDLPTADDPVELTNENTPLKANGMLYACTAHSKVLALDPDTGKE 250 Query: 247 KWHYDPELKTN---ESFQHVTCRGVSYHE----AKAETASPEVMAD--------CPRRII 291 W +DP++K+ + F H+TCRGVSY++ AK+E+A+ V+++ CPRR+ Sbjct: 251 LWRFDPQIKSPVGFKGFAHMTCRGVSYYDEAAYAKSESAASAVISEAGKAVAQACPRRLY 310 Query: 292 LPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGS 351 LP D RLIA+NA+ GK+CE F GV++L + G Y TSP IT ++M G Sbjct: 311 LPTADARLIALNADTGKICEGFGKNGVVDLTQGIGPFTAGGYYSTSPAAITRDLVIMGGH 370 Query: 352 VTDNFSTRETSGVIRGFDVNTGELLWAFD---PGAKDPNAIPSDEHTFTFNSPNSWAPAA 408 VTDN ST E SGVIR FDV+ G L+W +D P A +P +P EH ++ NS N W+ A+ Sbjct: 371 VTDNESTNEPSGVIRAFDVHDGHLVWNWDSNNPDATEP--LPEGEH-YSRNSANMWSLAS 427 Query: 409 YDAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMD 468 D KL +VYLP+G TPD WG +RTP E++++ ++AL+ TGK+ W+YQ HHDLWDMD Sbjct: 428 VDEKLGMVYLPLGNQTPDQWGADRTPGAEKFSAGLVALDLATGKVRWNYQFTHHDLWDMD 487 Query: 469 LPAQPTLADI-TVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVT 527 + +QPTL D+ T +G K P + AP K G+++VLDRR+G ++P E P PQGA KGD Sbjct: 488 VGSQPTLLDMKTADGVK-PALIAPTKQGSLYVLDRRDGTPIIPIKEIPAPQGAVKGDRTA 546 Query: 528 PTQPFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNL 587 PTQ S+L+ +L+ MWGA+ FDQ++CR+ F ++RYEG +TPPSEQG+L++PGN+ Sbjct: 547 PTQARSDLNLL-APELTEKAMWGASPFDQMLCRIQFKELRYEGQYTPPSEQGSLIYPGNV 605 Query: 588 GMFEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGV 647 G+F WGG+SVDP R++ +P + FVSK++PR E D+K +G+QP G Sbjct: 606 GVFNWGGVSVDPVRQMLFTSPNYMAFVSKMVPRA-----EVAADSKRESETAGVQPNTGA 660 Query: 648 PYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNM 707 PY V ++PF+SP G+PC+ PAWGY++ +DL T++VVWK++ GT +DS P P+ +P + Sbjct: 661 PYAVIMHPFMSPLGVPCQAPAWGYVAGIDLTTSKVVWKRKNGTSRDSSPLPIGLP----L 716 Query: 708 GMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYE-VNGKQ 766 G+P +GG + TAG V F++ T D YLRAY+++ G +LW+ RLPAGGQATPMTY +GKQ Sbjct: 717 GVPSMGGSMVTAGGVGFLSGTLDQYLRAYDVNTGNELWKSRLPAGGQATPMTYTGKDGKQ 776 Query: 767 YVVISAGGHGSFGTKMGDYIVAYALPD 793 YV++ GGHGS GTKMGDY++AY L + Sbjct: 777 YVLLVVGGHGSLGTKMGDYVIAYKLSE 803 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: 2170 Number of extensions: 130 Number of successful extensions: 14 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: 803 Length adjustment: 41 Effective length of query: 755 Effective length of database: 762 Effective search space: 575310 Effective search space used: 575310 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