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_052236884.1 FPB0191_RS08270 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase
Query= BRENDA::Q70JN9 (743 letters) >NCBI__GCF_000807275.1:WP_052236884.1 Length = 803 Score = 432 bits (1110), Expect = e-125 Identities = 241/662 (36%), Positives = 355/662 (53%), Gaps = 48/662 (7%) Query: 104 ASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPRPGQTNKWAAETTPIKV 163 A+ DW AYG ++ + YS L++I P N +L+ + TG P + E TP+KV Sbjct: 158 AAEDWIAYGGTNAGLHYSALNQIVPNNIHKLQEVWRIRTGDMPTADDPVELTNENTPLKV 217 Query: 164 GDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTAA----------CKGVTYFTS 213 D LY C+A ++ ++P TGK +W+ + AI + A C+G++Y+ S Sbjct: 218 NDKLYTCTAHGWVLALEPETGKTLWKFD-----PAISNSGAGTFKGWAHMTCRGLSYYDS 272 Query: 214 SQV------------PEGQPCHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGL 261 + + C RI T D RLIA++A G LC+ FG GQV+L QG+ Sbjct: 273 DRYLKQFAKDKIALKVKSSSCPRRIYLPTADARLIALNADNGQLCDSFGVNGQVDLTQGI 332 Query: 262 GESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPN 321 G+ PG T+P V +V+V V D + PSGV+R +D G +W WD P+ Sbjct: 333 GKFTPGGYYSTSPALVTKQLVIVGGHVTDNESTNEPSGVVRAFDIYDGHLVWNWDSGNPD 392 Query: 322 DHSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAVVA 381 + + Y+R +PN W+ + D ALGLVY+P GN D Y R+P K ++ +VA Sbjct: 393 ATTPLPKDKKYTRNSPNVWSITSADEALGLVYLPLGNQTPDQYGGNRTPVVEKYAAGIVA 452 Query: 382 LDVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLDRRD 441 LD+ +G W +Q H D+WD D+ +Q L+D+ G PA+I PTK+G +VL+R+ Sbjct: 453 LDITSGKVVWNYQFTHHDLWDMDVPAQPILVDLKTTQGIE-PAVIQPTKQGSLYVLNRKT 511 Query: 442 GKPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGMSPIDQLFCRIK 501 G+PI+P+ E P G + GD SPTQ + L P L+E DMWG +P DQL CRIK Sbjct: 512 GQPIVPINEVSVPQ-GAVKGDWTSPTQ--ARSQLNLLPPPLREQDMWGATPFDQLSCRIK 568 Query: 502 FRRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQLVTRK 561 F+ Y G++TPPS+ I YPG G +WG V+ DP I+ A+ N +L+ + Sbjct: 569 FKSLRYEGQYTPPSLQGSLI-YPGNVGVMNWGGVAIDPVRKIIFASPNYMAFTSKLIPQA 627 Query: 562 KADELGLMPIDDPNYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTGMMCNRPPYGMITAI 621 + +P ++ N G G GA PY + + PF G C P +G + I Sbjct: 628 E------VPKNEANASEGAGLQPNQGA----PYAVRIQPFL-SLVGFPCQAPSWGNVAGI 676 Query: 622 DMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQIR 681 ++ + + W HP GT+R N P+ +P LP+ +G P GG + TAGGV F++ D +R Sbjct: 677 NLAN-NSIAWIHPNGTSRDNTPF-IP--LPFPVGVPAMGGPMTTAGGVAFLSGTLDQYLR 732 Query: 682 AIDEHTGKVVWSAVLPGGGQANPMTY-EANGHQYVAIMAGGHHFMMTPVSDQLVVYALPD 740 A D GK +WS+ LP GGQA PMT+ + QY+ ++ GGH T + D ++ YALP Sbjct: 733 AYDITNGKEIWSSRLPAGGQATPMTFWGKDNRQYIVLVVGGHGSFGTKMGDYIIAYALPK 792 Query: 741 HK 742 +K Sbjct: 793 NK 794 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: 1977 Number of extensions: 125 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: 803 Length adjustment: 41 Effective length of query: 702 Effective length of database: 762 Effective search space: 534924 Effective search space used: 534924 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