Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_025329713.1 SALWKB2_RS00315 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase
Query= BRENDA::D4P700 (796 letters) >NCBI__GCF_000600005.1:WP_025329713.1 Length = 792 Score = 960 bits (2481), Expect = 0.0 Identities = 459/800 (57%), Positives = 590/800 (73%), Gaps = 18/800 (2%) Query: 3 KNSSSFSVVRFLTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSA 62 K +SFS+ R +T++ LT ++LIGGIWL +GGS +Y I + L L + S+ Sbjct: 2 KAYTSFSLARIMTLIVLWLTVIYLLIGGIWLIWLGGSAFYAIIALILCLFTTLYHYQRSS 61 Query: 63 ALVVYALLLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGLYQPGKGALGA 122 L +YA+ L TL WG+WE GTDFWALAPR D+L +FG+WL+ P+ R + G L Sbjct: 62 CLWLYAITLFITLIWGLWESGTDFWALAPRFDLLFLFGLWLLTPWPTRHISASRSGKL-I 120 Query: 123 MGVALVASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRF 182 + +AL+A +V+ YS+ +DPQ +NG + AP A + +A DWPAY R Q GTR+ Sbjct: 121 ITLALIAILSVMFYSISHDPQQINGTI-TRLQPAPAADD-NGVAAEDWPAYGRTQGGTRY 178 Query: 183 SPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALD 242 SPL QIN NVK+L+VAW ++TGD K +D E T+E+TPIKI L++CTPHQ L ALD Sbjct: 179 SPLTQINTANVKQLKVAWTYRTGDFKTTNDSAETTNELTPIKIGKKLFICTPHQFLDALD 238 Query: 243 AATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVNDGRL 302 A TGK+ W+FDP L++N TFQH+TCRGVSY++ A + T A+C +++ LPVNDGRL Sbjct: 239 ATTGKRLWRFDPELRSNRTFQHLTCRGVSYYDATTAHSSETTASAICPQKVLLPVNDGRL 298 Query: 303 FALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDNFSTR 362 A++A+TG++CP FG+NGE++LQ K P G Y PTSPPV+T +TI++ G+VTDN ST+ Sbjct: 299 IAVNAQTGQKCPDFGHNGEINLQAKMPYAFLGGYNPTSPPVVTPSTIIIGGSVTDNLSTK 358 Query: 363 EPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDIVYLP 422 EPSG IRG+DVN G+L WVFD GA++PNA+P ++ F NSPN+WAP YD + +IVY+P Sbjct: 359 EPSGVIRGYDVNNGQLKWVFDTGAENPNAMPGEKTNFVHNSPNAWAPLAYDQQRNIVYIP 418 Query: 423 MGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTLADIT 482 GV+TPDIWGG+R +ERYA+S++ALNA+TGKL+W +QT HHDLWDMD+P+QP+L DIT Sbjct: 419 TGVSTPDIWGGHRNKLKERYANSLVALNASTGKLLWHFQTTHHDLWDMDVPAQPSLMDIT 478 Query: 483 DKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQ-----GAAKGDHVSATQPYS 537 G + IY KTGNIFVL+R TG+ +VP E VPQ +G+H +ATQP+S Sbjct: 479 IPSGKRIAAIYVLTKTGNIFVLNRETGQPIVPVTEQSVPQTLKHGKPTQGEHYAATQPFS 538 Query: 538 ELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFEWG 597 L+ PK LTDKDMWGATM+DQL+CR+ FKRL Y G +TPPSE GTLVFPGNLG+FEWG Sbjct: 539 ALSLMPKDKLTDKDMWGATMFDQLLCRIQFKRLNYNGIYTPPSENGTLVFPGNLGVFEWG 598 Query: 598 GISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPYGVE 657 GISV+ RQIA+ NP+ LPFVS+LIP P ++ G+GTE GIQP YG PYGVE Sbjct: 599 GISVNQDRQIALMNPIGLPFVSRLIPANPDRAQQKQ-----GAGTENGIQPMYGAPYGVE 653 Query: 658 LNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSP----VPLPFKMGMPML 713 ++PFLSP GLPCKQPAWG+V+ VDL+TN+VVWK+RIGT+RDS P +P P K+G+P L Sbjct: 654 ISPFLSPIGLPCKQPAWGFVAGVDLQTNQVVWKKRIGTIRDSLPKLFELP-PLKIGVPGL 712 Query: 714 GGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTYEVNGKQYVVIAA 773 GG ++TAG + F+ AT DNYLRA+ T G+LLWQ RLPAGGQATPMTY VNGKQYVV A Sbjct: 713 GGSISTAGNIMFVSATQDNYLRAYDTSNGDLLWQTRLPAGGQATPMTYAVNGKQYVVQMA 772 Query: 774 GGHGSFGTKLGDYVIAYALP 793 GGH SFGTK+GDY+IAY LP Sbjct: 773 GGHSSFGTKMGDYLIAYTLP 792 Lambda K H 0.319 0.137 0.433 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: 2315 Number of extensions: 133 Number of successful extensions: 16 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: 792 Length adjustment: 41 Effective length of query: 755 Effective length of database: 751 Effective search space: 567005 Effective search space used: 567005 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