Align fructokinase (EC 2.7.1.4) (characterized)
to candidate BPHYT_RS09175 BPHYT_RS09175 2-dehydro-3-deoxygluconokinase
Query= BRENDA::Q42645 (331 letters) >FitnessBrowser__BFirm:BPHYT_RS09175 Length = 312 Score = 132 bits (332), Expect = 1e-35 Identities = 99/316 (31%), Positives = 154/316 (48%), Gaps = 20/316 (6%) Query: 14 VVSFGEMLIDFVPTSSGVSLAEAPGFLKAPGGAPANVAIAVSRLGGNAAFVGKLGDDEFG 73 +++ GE +I+F S + P +L+ GG +N IA +R G FV +G D FG Sbjct: 12 ILALGEAMIEF-----NQSAKDQPNYLQGFGGDTSNFCIAAARQGAQTGFVSAVGADHFG 66 Query: 74 HMLAGILKKNGVSADGLSFDKGARTALAFVTLKSDGEREFMFYRNPSADMLLTPDELNLD 133 +L + ++ V + D A T + FV+ +G F + R SA P +L LD Sbjct: 67 RLLVDLWEREQVDTSLVRVDPQASTGVYFVSHGPNG-HAFDYLRAGSAASRYAPHDLPLD 125 Query: 134 LIRSAKVFHYGSIRLIVE-PCRSAHLKAMEEAKKAGALLSYDPNLRLPLWPSAEEAREQI 192 I +AKV H I L + A L+A+ A+ G +S+D NLRL LWP A AR + Sbjct: 126 AIAAAKVIHLSGISLAISLSACDAALEAIAHARANGVRVSFDTNLRLKLWPLA-RARAVM 184 Query: 193 MSIWDKAEVIKVSDNELEFLTGNSTIDDATAMSLWHPNLKLLLVTLGDQGCRYYTKNFKG 252 + + ++ S +++ LTG + D+ L H ++ + LG +G T N + Sbjct: 185 LEAIRQTDICLPSWDDVTDLTGLTGRDEIVDFLLSH-GPSVVALKLGKEGSYIATPNERR 243 Query: 253 SLDGFKVNAVDTTGAGDSFVGALLNKIV--DDHSIIEDESRLKEVLKFANACGAITTTKK 310 + G VNAVD TGAGD F GA + +IV DD ++AN A++T Sbjct: 244 VVPGHVVNAVDATGAGDCFGGAFIARIVAGDDPF---------TAARYANVAAALSTQGY 294 Query: 311 GAIPALPTVADALELI 326 GA+ +P+ A +L+ Sbjct: 295 GAVAPIPSRATVEQLL 310 Lambda K H 0.316 0.134 0.385 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: 245 Number of extensions: 15 Number of successful extensions: 4 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: 331 Length of database: 312 Length adjustment: 28 Effective length of query: 303 Effective length of database: 284 Effective search space: 86052 Effective search space used: 86052 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: 41 (21.6 bits) S2: 48 (23.1 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