Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate WP_086511089.1 BZY95_RS17045 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family
Query= BRENDA::Q70JN9 (743 letters) >NCBI__GCF_002151265.1:WP_086511089.1 Length = 812 Score = 519 bits (1336), Expect = e-151 Identities = 278/669 (41%), Positives = 380/669 (56%), Gaps = 21/669 (3%) Query: 83 DIGSMDPNDVPQMAPQQSASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHT 142 D G P A Q +P DW AYG + R+SP ITP NADQL+VA+ ++T Sbjct: 153 DSGPDAPTTAAAEAIPQQDAPNDTDWVAYGGTNLAQRFSPADRITPHNADQLEVAWEFNT 212 Query: 143 GSYPRPGQTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIP-- 200 G P P +A + TP+K+G+ LY+C+ N + +DP TG++ W + EA Sbjct: 213 GDEP-PSDAAPYAFQNTPLKIGNSLYVCTQSNQVFALDPGTGEQQWHFDPEVAVEAQEHV 271 Query: 201 YTAACKGVTYFTSSQVPEGQPCHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQG 260 ++ C+ V YF + E C R+L GTLD RL+A++A G+LC FG+ G V+L Sbjct: 272 FSTTCRAVAYFEAPDPVE--ECPRRLLLGTLDGRLMALNAEDGSLCNSFGDNGTVDLNDR 329 Query: 261 LGESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNRP 320 + G +S T+ P VVNG+VVV H+V D QRR APSG +R YDA +G++ W WD Sbjct: 330 MDPQALGLLSNTSGPIVVNGIVVVGHQVTDNQRRDAPSGAVRAYDAITGEWQWTWDSVWT 389 Query: 321 NDHSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAVV 380 QP Y RGTPN W A++ D LGLVY+PTGN +D Y RSPEE++ +S +V Sbjct: 390 TPDQQPPEGELYPRGTPNVWTAISADEELGLVYLPTGNPTNDQYGGDRSPEEDEFTSTLV 449 Query: 381 ALDVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLDRR 440 A++ +G RW F TV D+WDYD+G+Q L+D P DG P PA++ TK GQ FV DR Sbjct: 450 AVEADSGEVRWKFTTVLHDLWDYDLGAQPALIDFPTDDG-PRPAVVQATKYGQVFVFDRE 508 Query: 441 DGKPILPVEERPAPSPGVIPGD------PRSPTQPWSTGMPALRVPDLKETDMWGMSPID 494 G+P+LP+EERP P G I GD SP+ P +P V WG +PID Sbjct: 509 TGEPLLPIEERPVPQ-GAIEGDWTAEVQRFSPSMPNFGSIPGQEVEHFTGAHTWGATPID 567 Query: 495 QLFCRIKFRRANYTGEFTPPSVDKP--WIEYPGYNGGSDWGSVSYDPQSGILIANWNITP 552 L+CRI+F R Y G FTPP++D +++P GG +WGS ++D +G++I N N P Sbjct: 568 HLYCRIQFERMRYEGMFTPPTLDHAGGMLQFPAILGGINWGSAAFDLDNGLMIVNNNRMP 627 Query: 553 MYDQLVTRKKADEL-GLMPIDDPNYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTGMMCN 611 L R++ADE+ + PI + + A+ M G P W M C Sbjct: 628 SRVVLYPREEADEMENIAPIGEEDASYIDQEAQ---PMLGAPVA-AQRGAWLSPLDMPCA 683 Query: 612 RPPYGMITAIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVF 671 PP+G ++A D+ G+ ++W P+GT+ GPWG+P L +G P + G V TAGGV F Sbjct: 684 APPWGFLSATDLASGE-LVWSRPIGTSFDQGPWGIPARLKMTVGAPTSAGPVTTAGGVTF 742 Query: 672 IAAATDNQIRAIDEHTGKVVWSAVLPGGGQANPMTYEANGHQYVAIMAGGHHFMMTPVSD 731 I A D+ IRA + TG ++W A LP GGQA PMTY G QYV I AGG T + D Sbjct: 743 IGATMDDYIRAFNNTTGDMLWEARLPAGGQATPMTYMHEGRQYVVIAAGGAFQAETSLGD 802 Query: 732 QLVVYALPD 740 ++ YALP+ Sbjct: 803 SVMAYALPE 811 Lambda K H 0.315 0.134 0.428 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: 2094 Number of extensions: 133 Number of successful extensions: 9 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: 743 Length of database: 812 Length adjustment: 41 Effective length of query: 702 Effective length of database: 771 Effective search space: 541242 Effective search space used: 541242 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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