Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate WP_007678368.1 BN137_RS04255 pyrroloquinoline quinone-dependent dehydrogenase
Query= CharProtDB::CH_002195 (796 letters) >NCBI__GCF_000319285.1:WP_007678368.1 Length = 698 Score = 398 bits (1023), Expect = e-115 Identities = 243/660 (36%), Positives = 348/660 (52%), Gaps = 34/660 (5%) Query: 143 PQEINGTLSADAT-PAEAISPVADQDWPAYGRNQEGQRFSPLKQINADNVHNLKEAWVFR 201 P + +G A A+ PA + P + W ++ Q++SPL QI +NV L + W F Sbjct: 64 PDKADGQNVASASQPATPLVP-SSATWDSFHGQLNAQKYSPLTQITPENVGKLTKVWEFH 122 Query: 202 TGDVKQ-PNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGKEKWHYDPELKTNESF 260 TGDV D TPI DT+Y+ T RL ALD +GKEKWHYD + Sbjct: 123 TGDVSDGKGDTPATVWSATPIFANDTIYIGTPFDRLIALDPGTGKEKWHYDTKSSRKALT 182 Query: 261 QHVTC-RGVSYHEAKAETASPEVMADCPRRIILPVNDGRLIAINAENGKLCETFANKGVL 319 Q V RGVSY +AK +P C + + L DG+L A++A++GK C FA+ GVL Sbjct: 183 QPVLKNRGVSYWQAK----NPVAGEACQKIVYLGTVDGKLFALDADSGKPCTGFADNGVL 238 Query: 320 NL-QSNMPDTKPGLYEPTSPPIITDKTIVMAGSVTDNFSTRETSGVIRGFDVNTGELLWA 378 N+ Q N + K L PP + +++ + D G I + TGE W Sbjct: 239 NVNQWNTINAKFPL-SILQPPTVVGNHLLVGWAGKDWAYAEAPPGTIFSINAQTGEREWT 297 Query: 379 FDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKLDLVYLPMGVTTPDIWGGNRTPEQER 438 F+ AIP + T + N W + D LVYLP+ +P+ WGGNR + Sbjct: 298 FE-------AIPEEIRKQT-GTANVWTHMSADEANGLVYLPVSSPSPNYWGGNRV-KAIP 348 Query: 439 YASSILALNATTGKLAWSYQTVHHDLWDMDLPAQPTLADITVNGQKVPVIYAPAKTGNIF 498 +S AL+ TGK+ WS Q VHHD+WD D+ + PTL DITVNG+ +P + K G +F Sbjct: 349 LGTSTTALDINTGKVVWSRQWVHHDVWDYDINSAPTLMDITVNGKAIPALVQATKQGFLF 408 Query: 499 VLDRRNGELVVPAPEKPVPQ--GAAKGDYVTPTQPFSELSFRPTKDLSGADMWG-ATMFD 555 V++R GE V P E+PVPQ G+ KG+ ++PTQPF ++W A + Sbjct: 409 VVNRLTGEDVWPIEERPVPQGDGSVKGEVLSPTQPFPTRPAPLLDQSKKPEIWKLADIVG 468 Query: 556 QLVCRVMFHQMRYEGIFTPPSE--QGTLVFPGNLGMFEWGGISVDPNREVAIANPMALPF 613 C ++ + YEG++TPP+ +G L +P + G +WGG++ DP +++AI N + Sbjct: 469 AGQCSRLWDNLTYEGMYTPPTTKGEGALTYPDSAGGVQWGGVAFDPKKQIAIVNTSHIVQ 528 Query: 614 VSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGVPYGVTLNPFLSPFGLPCKQPAWGYIS 673 KL R + K K G E+G PQ G PYG+ L + G+PC QP +G I Sbjct: 529 YVKLYSR-----EDYDKADKSAGNENGFAPQEGAPYGMRLLVANNWLGMPCWQPPFGEIV 583 Query: 674 ALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLGGPISTAGNVLFIAATADNYL 733 ALD+ T EV W++ +G Q F +P + G P +GGP TAG V+FI A+ D + Sbjct: 584 ALDMHTGEVKWRRPVGASQQYGFF-----MPESWGSPTIGGPAITAGGVIFIGASMDAKV 638 Query: 734 RAYNMSNGEKLWQGRLPAGGQATPMTYEVNGKQYVVISAGGHGSFGTKMGDYIVAYALPD 793 RAY++ +GE+LW ++ A A P YE G+QYV AGG+ ++GD +V YALP+ Sbjct: 639 RAYSVDSGEELWSDQVEAPAVANPSVYEYKGRQYVAFVAGGNTILKDQVGDQVVVYALPE 698 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: 1962 Number of extensions: 122 Number of successful extensions: 17 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: 698 Length adjustment: 40 Effective length of query: 756 Effective length of database: 658 Effective search space: 497448 Effective search space used: 497448 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 24 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