Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate BPHYT_RS08325 BPHYT_RS08325 glucose dehydrogenase
Query= BRENDA::Q70JN9 (743 letters) >FitnessBrowser__BFirm:BPHYT_RS08325 Length = 837 Score = 451 bits (1159), Expect = e-131 Identities = 258/700 (36%), Positives = 353/700 (50%), Gaps = 72/700 (10%) Query: 96 APQQSASPASG----DWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPRPGQT 151 AP A SG DW AYG RYSPL +ITP+N L+VA+ + TG P Sbjct: 152 APASGAGAGSGIDPADWPAYGRTQEGTRYSPLQQITPENVKDLQVAWTFRTGDMKGPNDP 211 Query: 152 NKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTAACKGVTYF 211 + E TPIK+GD LY+CS + +D TG W+ + K + C+GV+Y Sbjct: 212 VEITDEVTPIKIGDLLYLCSPHQILFALDAKTGTLKWKFDPRLKSDPSFQHVTCRGVSYV 271 Query: 212 -------------------------------------------TSSQVPEGQP------- 221 T++ P P Sbjct: 272 DLSAGATAAAPATAPASDATATAAAPASDTATAAAPASDTATATTTAAPAATPASDTTAT 331 Query: 222 CHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGLGESVPGFVSMTTPPPVVNGV 281 C RI D L A+DA TG CEGF N G ++L + G T+P + + V Sbjct: 332 CTRRIYLPVNDGHLYALDALTGQRCEGFANHGDLDLQHAQPVTTAGMYEPTSPSIITSKV 391 Query: 282 VVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPNDHSQPTGNNHYSRGTPNSWA 341 ++V V D PSGVIRG+D +G+ LWA+D + + P HY+ +PNSWA Sbjct: 392 IIVAGSVEDNFSNREPSGVIRGFDVRTGELLWAFDPGAKDPNHIPGAGEHYTWNSPNSWA 451 Query: 342 AMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAVVALDVKTGSPRWVFQTVHKDVW 401 D L +VY+P G + D + R+PE+ + +S ++AL+ TG W +QT H D+W Sbjct: 452 PAAYDAKLDIVYLPMGVTTPDIWGGNRTPEQERYASGLLALNASTGKLAWFYQTAHHDLW 511 Query: 402 DYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLDRRDGKPILPVEERPAPSPGVIPG 461 D D SQ TL D+ G+DGQ VP + P K G FVLDRR G P++P E P P G PG Sbjct: 512 DMDQPSQPTLADITGKDGQSVPVVYAPAKTGNLFVLDRRTGVPVVPAPETPVPQ-GAAPG 570 Query: 462 DPRSPTQPWS--TGMPALRVPDLKETDMWGMSPIDQLFCRIKFRRANYTGEFTPPSVDKP 519 D SPTQP+S T P+ ++ D DMWG + DQL CR+ F + Y G FTPPS+ Sbjct: 571 DHVSPTQPFSQLTYRPSKKLTD---ADMWGATMYDQLVCRVMFHKLRYEGTFTPPSLQGT 627 Query: 520 WIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQLVTRKKADELGLMPIDDPNYKPG 579 + +PG G +WG ++ D I +AN P +L+ R + P++ G Sbjct: 628 LV-FPGNLGMFEWGGIAVDTDRQIAVANPIALPFVSRLIPRGPGN-----PLEPVPGAKG 681 Query: 580 GGGAEGNGAMDGTPYGIVVTPFWDQYTGMMCNRPPYGMITAIDMKHGQKVLWQHPLGTAR 639 G G G PYG+V+ F + G+ C +P +G I+AID+K + ++W+ +GT R Sbjct: 682 SGTESGIQPQYGVPYGVVINAFLSPF-GLPCKQPAWGYISAIDLKTNE-IVWKKRIGTVR 739 Query: 640 ANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQIRAIDEHTGKVVWSAVLPGG 699 + P +P LP+ +G P GG +VTAGGV FI A DN IR D + GK VW A LP G Sbjct: 740 DSSP--IP--LPFRMGMPMLGGPIVTAGGVAFIGATADNYIRGFDVNNGKQVWEARLPAG 795 Query: 700 GQANPMTYEANGHQYVAIMAGGHHFMMTPVSDQLVVYALP 739 GQA PM+Y NG QY+ I AGGH T + D ++ YALP Sbjct: 796 GQATPMSYSINGRQYLVIAAGGHGSFGTKLGDYVIAYALP 835 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: 2179 Number of extensions: 164 Number of successful extensions: 13 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 5 Number of HSP's successfully gapped: 2 Length of query: 743 Length of database: 837 Length adjustment: 41 Effective length of query: 702 Effective length of database: 796 Effective search space: 558792 Effective search space used: 558792 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