Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate BWI76_RS04950 BWI76_RS04950 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family
Query= CharProtDB::CH_002195 (796 letters) >FitnessBrowser__Koxy:BWI76_RS04950 Length = 796 Score = 1496 bits (3873), Expect = 0.0 Identities = 713/796 (89%), Positives = 750/796 (94%) Query: 1 MAINNTGSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRS 60 MA + RLLVTLTALFAA CGLYLL GG WLVA+GGSWYYP+AGLVML V +L+R Sbjct: 1 MAETKSQQSRLLVTLTALFAAFCGLYLLAGGAWLVALGGSWYYPVAGLVMLAVTVLLFRG 60 Query: 61 KRAALWLYAALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGA 120 KR+ALWLYAALLL TMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRL IP+SGA Sbjct: 61 KRSALWLYAALLLATMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLPIPSSGA 120 Query: 121 VAALVVALLISGGILTWAGFNDPQEINGTLSADATPAEAISPVADQDWPAYGRNQEGQRF 180 VA LVVALLISGGILTWAGFNDPQE+NGTLSADATPA IS VAD DW AYGRNQEGQR+ Sbjct: 121 VAGLVVALLISGGILTWAGFNDPQEVNGTLSADATPAAPISEVADGDWSAYGRNQEGQRY 180 Query: 181 SPLKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALD 240 SPLKQINADNV NLKEAWVFRTGD+KQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALD Sbjct: 181 SPLKQINADNVKNLKEAWVFRTGDLKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALD 240 Query: 241 AASGKEKWHYDPELKTNESFQHVTCRGVSYHEAKAETASPEVMADCPRRIILPVNDGRLI 300 AA+GKEKWH+DP+L + SFQHVTCRGVSYHEAKA+ A +V+ADCPRRIILPVNDGRL Sbjct: 241 AATGKEKWHFDPQLNADPSFQHVTCRGVSYHEAKADNAPADVVADCPRRIILPVNDGRLF 300 Query: 301 AINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSVTDNFSTRE 360 AINAE GKLCE+FANKG+LNLQ+NMP T PG+YEPTSPPIITDKTIV+AG+VTDNFSTRE Sbjct: 301 AINAETGKLCESFANKGILNLQTNMPVTTPGMYEPTSPPIITDKTIVIAGAVTDNFSTRE 360 Query: 361 TSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKLDLVYLPM 420 SGVIRGFDVNTG+LLWAFDPGAKDPNAIP DEH FT NSPNSWAPAAYDAKLDLVYLPM Sbjct: 361 PSGVIRGFDVNTGKLLWAFDPGAKDPNAIPDDEHHFTLNSPNSWAPAAYDAKLDLVYLPM 420 Query: 421 GVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPAQPTLADITV 480 GVTTPDIWGGNRTPEQERYASSI+ALNATTGKLAWSYQTVHHDLWDMD+P+QPTLADI V Sbjct: 421 GVTTPDIWGGNRTPEQERYASSIVALNATTGKLAWSYQTVHHDLWDMDMPSQPTLADIDV 480 Query: 481 NGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPTQPFSELSFRPT 540 NG+ VPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYV TQPFS+LSFRP Sbjct: 481 NGKTVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVAKTQPFSDLSFRPK 540 Query: 541 KDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGMFEWGGISVDPN 600 KDL+GADMWGATMFDQLVCRV+FHQ+RYEGIFTPPSEQGTLVFPGNLGMFEWGGISVDPN Sbjct: 541 KDLTGADMWGATMFDQLVCRVIFHQLRYEGIFTPPSEQGTLVFPGNLGMFEWGGISVDPN 600 Query: 601 REVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGVPYGVTLNPFLSPF 660 R+VAIANPMALPFVSKLIPRGPGNPMEQPKDAKG+GTE+GIQPQYGVPYGVTLNPFLSPF Sbjct: 601 RQVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGSGTEAGIQPQYGVPYGVTLNPFLSPF 660 Query: 661 GLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLGGPISTAG 720 GLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDS+PFPMPV +PF MGMPMLGGPISTAG Sbjct: 661 GLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSLPFPMPVKLPFTMGMPMLGGPISTAG 720 Query: 721 NVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYEVNGKQYVVISAGGHGSFGT 780 NVLFI ATADNYLRAYNMSNGEKLWQ RLPAGGQATPMTYEVNGKQYVVISAGGHGSFGT Sbjct: 721 NVLFIGATADNYLRAYNMSNGEKLWQARLPAGGQATPMTYEVNGKQYVVISAGGHGSFGT 780 Query: 781 KMGDYIVAYALPDDVK 796 KMGDYIVAYALPDD K Sbjct: 781 KMGDYIVAYALPDDAK 796 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: 2669 Number of extensions: 139 Number of successful extensions: 4 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: 796 Length adjustment: 41 Effective length of query: 755 Effective length of database: 755 Effective search space: 570025 Effective search space used: 570025 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