Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate AO353_16045 AO353_16045 glucose dehydrogenase
Query= CharProtDB::CH_002195 (796 letters) >FitnessBrowser__pseudo3_N2E3:AO353_16045 Length = 803 Score = 756 bits (1953), Expect = 0.0 Identities = 380/804 (47%), Positives = 530/804 (65%), Gaps = 31/804 (3%) Query: 10 RLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALWLYA 69 RLL +L + L GL LL GG L +GGS YY +AG+ ++ +L ++RAAL LYA Sbjct: 11 RLLPSLLGIVLLLMGLALLAGGIKLSMLGGSLYYLLAGIGLVLTGILLLAARRAALGLYA 70 Query: 70 ALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGAV--AALVVA 127 +L + +W +WE+G D+W L PR + G+ L+LP+ R L+ + + AAL VA Sbjct: 71 VVLFASTVWALWEIGLDWWQLVPRLSLWFALGVVLLLPWFRRPLLRDGAAPLGTAALSVA 130 Query: 128 LLISGGILTWAGFNDPQEINGTLSADATPAEAISPVADQ-DWPAYGRNQEGQRFSPLKQI 186 ++++G + F P EI G L D + +P + +W AYGR + G R+SPLKQI Sbjct: 131 VVLAGATAVASQFTHPGEIMGELGRDTADMTSTAPAMPEGEWQAYGRTEFGDRYSPLKQI 190 Query: 187 NADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGKE 246 NV L+EAW RTGD+ +DP E+TNE TP+KV LY CTAH ++ ALD +GKE Sbjct: 191 TPANVGKLQEAWRIRTGDLPTADDPVELTNENTPLKVNGMLYACTAHSKVLALDPDTGKE 250 Query: 247 KWHYDPELKTN---ESFQHVTCRGVSYHE----AKAETASPEVMAD--------CPRRII 291 W +DP++K+ + F H+TCRGVSY++ AKA+ AS V+++ CPRR+ Sbjct: 251 LWRFDPQIKSPVGFKGFAHMTCRGVSYYDENAYAKADNASSAVISEAGKAVAQACPRRLY 310 Query: 292 LPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGS 351 LP D RLIA+NA+ GK+CE F + GV++L + PG Y TSP IT ++M G Sbjct: 311 LPTADARLIALNADTGKVCEGFGDHGVVDLTQGIGPFTPGGYYATSPAAITRDLVIMGGH 370 Query: 352 VTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDA 411 VTDN ST E SGVIR FD+ G L+W +D G + + T+T NSPN W+ A+ D Sbjct: 371 VTDNESTNEPSGVIRAFDIRDGHLVWNWDSGNPEATEPLAPGKTYTRNSPNMWSLASVDE 430 Query: 412 KLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPA 471 KL +VYLP+G PD WG +RTP E++++ ++AL+ TGK+ W++Q HHDLWDMD+ + Sbjct: 431 KLGMVYLPLGNQMPDQWGADRTPGAEKFSAGMVALDLATGKVRWNFQFTHHDLWDMDVGS 490 Query: 472 QPTLADI-TVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPTQ 530 QPTL D+ T +G K P + AP K G+++VLDRRNG +VP E P PQGA GD+ PTQ Sbjct: 491 QPTLLDMKTADGIK-PALIAPTKQGSLYVLDRRNGTPIVPIREVPAPQGAVTGDHTAPTQ 549 Query: 531 PFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGMF 590 S+L+ DL+ MWGA+ FDQ++CR+ F Q+RYEG +TPPS QG+L++PGN+G+F Sbjct: 550 ARSDLNLL-APDLTEKAMWGASPFDQMLCRIQFKQLRYEGQYTPPSLQGSLIYPGNVGVF 608 Query: 591 EWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGVPYG 650 WG +S+DP R++ +P + FVSKLIP+ E +K SG+QP G PY Sbjct: 609 NWGSVSLDPVRQMLFTSPNYMAFVSKLIPQA-----EVAAGSKRESETSGVQPNTGAPYA 663 Query: 651 VTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMP 710 VT++PF+SPFG+PC+ PAWGY++ +DL T++VVWK++ GT +DS P P+ +P+ G+P Sbjct: 664 VTMHPFMSPFGVPCQAPAWGYVAGIDLTTSKVVWKRKNGTSRDSSPLPIGLPI----GVP 719 Query: 711 MLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYE-VNGKQYVV 769 +GG I TAG V F++ T D YLRAY+++NG++LW+ RLPAGGQATPMTY +GKQYV+ Sbjct: 720 SMGGSIVTAGGVGFLSGTLDQYLRAYDVNNGKELWKSRLPAGGQATPMTYTGKDGKQYVL 779 Query: 770 ISAGGHGSFGTKMGDYIVAYALPD 793 + GGHGS GTKMGDY++AY L + Sbjct: 780 LVVGGHGSLGTKMGDYVIAYKLSE 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: 2182 Number of extensions: 136 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: 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