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_059150990.1 V474_RS07915 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family
Query= BRENDA::Q70JN9 (743 letters) >NCBI__GCF_001046635.1:WP_059150990.1 Length = 796 Score = 705 bits (1820), Expect = 0.0 Identities = 349/658 (53%), Positives = 447/658 (67%), Gaps = 22/658 (3%) Query: 91 DVPQMAPQQ---SASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPR 147 D+P + + S + DW AYG DS R+SPL +IT N LK A++ HTG P Sbjct: 152 DLPALGAEMGDPSLAATGDDWPAYGGSDSARRFSPLGQITAANVKDLKRAWLVHTGDMPS 211 Query: 148 -PGQTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTAACK 206 P + E TP+KVG+ LY+C+ +N ++ ++PA+GK+IWR + +AIPYTAAC+ Sbjct: 212 SPKIAKTYGGENTPLKVGNMLYVCTPKNIVLALNPASGKQIWRFDPKVSDDAIPYTAACR 271 Query: 207 GVTYFTSSQVPEGQPCHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGLGESVP 266 GV+Y+ P GQPC R++ GTLD RL A+DA TG C FG G+V+ G+G + P Sbjct: 272 GVSYYAVPNAPAGQPCAARLIFGTLDARLFAIDARTGARCTAFGANGEVDTKIGMGNTPP 331 Query: 267 GFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPNDHSQP 326 G+VS+ +PP +V GV V H+VLDGQ RWAPSGVIRGYDA +GK WAWD+ P + P Sbjct: 332 GYVSINSPPTIVRGVAVTGHQVLDGQDRWAPSGVIRGYDAVTGKLRWAWDMMHPEWNGYP 391 Query: 327 TGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAVVALDVKT 386 + RGTPN W +GD LGLVY+P GN+A+DYYS+LR P E + ++++VALDV T Sbjct: 392 PTGQIWERGTPNMWTIASGDEQLGLVYLPMGNAAADYYSSLRRPLEKEFATSLVALDVTT 451 Query: 387 GSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLDRRDGKPIL 446 G PRW FQ V DVWDYD G+QA+L+D G PAL++P+K+G +VLDRR GKP+ Sbjct: 452 GKPRWKFQAVRNDVWDYDFGAQASLVDYRG-----TPALVLPSKQGDIYVLDRRTGKPLT 506 Query: 447 PVEERPAPSPGVIPGDPRSPTQP---WSTGMPALRVPDLKETDMWGMSPIDQLFCRIKFR 503 P+ E AP GV P D R+ TQ W T LR P L E DMWGMSPIDQ+ CRI+FR Sbjct: 507 PIGELKAPGGGVEP-DQRAKTQRVSLWHT----LRKPALTERDMWGMSPIDQMVCRIQFR 561 Query: 504 RANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQLVTRKKA 563 +A+Y G FTPP ++ IEYPGYNGG+DWG V+ DP+ G+++AN+N P Y +LV R +A Sbjct: 562 KASYKGFFTPPESERRSIEYPGYNGGTDWGGVAIDPRRGVIVANYNDMPNYVRLVPRAEA 621 Query: 564 DELGLMPIDDPNYKPGGGGAEGNGAMDG-TPYGIVVTPFWD-QYTGMMCNRPPYGMITAI 621 ++ G P D + GGAEG G TPY I V W +TGM+C +PPYG I AI Sbjct: 622 NKKGWAPRDQA--RGNIGGAEGAGDPQAHTPYAIDVNAGWRLPFTGMLCKQPPYGGIRAI 679 Query: 622 DMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQIR 681 DMK G + +W PLGTAR NGP+G+P+ LP+ IGTPNNGGSVVTAGGV+F+AAATDN IR Sbjct: 680 DMKSG-RTIWDRPLGTARTNGPFGIPSMLPFNIGTPNNGGSVVTAGGVIFVAAATDNLIR 738 Query: 682 AIDEHTGKVVWSAVLPGGGQANPMTYEANGHQYVAIMAGGHHFMMTPVSDQLVVYALP 739 AID TGK +WS VLP GGQA PMTY NG QY+ I+ GGHHFM TP+ D+++ YALP Sbjct: 739 AIDLKTGKTLWSDVLPAGGQATPMTYSVNGKQYLVIVPGGHHFMETPIGDEVIAYALP 796 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: 2214 Number of extensions: 154 Number of successful extensions: 12 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: 796 Length adjustment: 41 Effective length of query: 702 Effective length of database: 755 Effective search space: 530010 Effective search space used: 530010 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