Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate PfGW456L13_4805 Glucose dehydrogenase, PQQ-dependent (EC 1.1.5.2)
Query= BRENDA::Q70JN9 (743 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4805 Length = 803 Score = 465 bits (1196), Expect = e-135 Identities = 263/674 (39%), Positives = 367/674 (54%), Gaps = 47/674 (6%) Query: 88 DPNDVPQMAPQQSASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPR 147 D D+ APQ GDW AYG + RYSPL +ITP N +L+ A+ TG P Sbjct: 156 DTADMTSTAPQMP----EGDWQAYGRSEFGDRYSPLKQITPANVGKLQEAWRIQTGDLPT 211 Query: 148 PGQTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEK----YEAIPYTA 203 + E TP+K LY C+A + ++ +DP TGKE+WR + K ++ + Sbjct: 212 ADDPVELTNENTPLKANGMLYACTAHSKVLALDPDTGKELWRFDPQIKSPVGFKGFAHMT 271 Query: 204 ACKGVTYF-----------TSSQVPEG-----QPCHNRILEGTLDMRLIAVDAATGNLCE 247 C+GV+Y+ S+ + E Q C R+ T D RLIA++A TG +CE Sbjct: 272 -CRGVSYYDEAAYAKSESAASAVISEAGKAVAQACPRRLYLPTADARLIALNADTGKICE 330 Query: 248 GFGNGGQVNLMQGLGESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAE 307 GFG G V+L QG+G G T+P + +V++ V D + PSGVIR +D Sbjct: 331 GFGKNGVVDLTQGIGPFTAGGYYSTSPAAITRDLVIMGGHVTDNESTNEPSGVIRAFDVH 390 Query: 308 SGKFLWAWDVNRPNDHSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSAL 367 G +W WD N P+ HYSR + N W+ + D LG+VY+P GN D + A Sbjct: 391 DGHLVWNWDSNNPDATEPLPEGEHYSRNSANMWSLASVDEKLGMVYLPLGNQTPDQWGAD 450 Query: 368 RSPEENKVSSAVVALDVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIM 427 R+P K S+ +VALD+ TG RW +Q H D+WD D+GSQ TL+DM DG PALI Sbjct: 451 RTPGAEKFSAGLVALDLATGKVRWNYQFTHHDLWDMDVGSQPTLLDMKTADGVK-PALIA 509 Query: 428 PTKRGQTFVLDRRDGKPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDM 487 PTK+G +VLDRRDG PI+P++E PAP G + GD +PTQ S L P+L E M Sbjct: 510 PTKQGSLYVLDRRDGTPIIPIKEIPAPQ-GAVKGDRTAPTQARSD--LNLLAPELTEKAM 566 Query: 488 WGMSPIDQLFCRIKFRRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIAN 547 WG SP DQ+ CRI+F+ Y G++TPPS ++ + YPG G +WG VS DP +L + Sbjct: 567 WGASPFDQMLCRIQFKELRYEGQYTPPS-EQGSLIYPGNVGVFNWGGVSVDPVRQMLFTS 625 Query: 548 WNITPMYDQLVTRKKADELGLMPIDDPNYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTG 607 N ++V R + D + G + N G PY +++ PF G Sbjct: 626 PNYMAFVSKMVPRAEV-------AADSKRESETAGVQPN---TGAPYAVIMHPFMSP-LG 674 Query: 608 MMCNRPPYGMITAIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAG 667 + C P +G + ID+ KV+W+ GT+R + P LP GLP +G P+ GGS+VTAG Sbjct: 675 VPCQAPAWGYVAGIDLT-TSKVVWKRKNGTSRDSSP--LPIGLP--LGVPSMGGSMVTAG 729 Query: 668 GVVFIAAATDNQIRAIDEHTGKVVWSAVLPGGGQANPMTYEA-NGHQYVAIMAGGHHFMM 726 GV F++ D +RA D +TG +W + LP GGQA PMTY +G QYV ++ GGH + Sbjct: 730 GVGFLSGTLDQYLRAYDVNTGNELWKSRLPAGGQATPMTYTGKDGKQYVLLVVGGHGSLG 789 Query: 727 TPVSDQLVVYALPD 740 T + D ++ Y L + Sbjct: 790 TKMGDYVIAYKLSE 803 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: 1969 Number of extensions: 145 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: 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 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