Align Fructokinase-1; ZmFRK1; EC 2.7.1.4 (characterized)
to candidate RR42_RS09470 RR42_RS09470 2-dehydro-3-deoxygluconokinase
Query= SwissProt::Q6XZ79 (323 letters) >FitnessBrowser__Cup4G11:RR42_RS09470 Length = 314 Score = 126 bits (316), Expect = 8e-34 Identities = 100/311 (32%), Positives = 148/311 (47%), Gaps = 14/311 (4%) Query: 8 VVSFGEMLIDFVPTVAGVSLAEAPAFLKAPGGAPANVAIAVSRLGGGAAFVGKLGDDEFG 67 VV+ GE ++ V AG L F K GA NVAI +SRLG + +LGDD Sbjct: 7 VVTLGEAMLMLVAGEAG-PLEGVQTFHKRTAGAETNVAIGLSRLGLKVGWASRLGDDSMA 65 Query: 68 RMLAAILRDNGVDDGGVVFDSGARTALAFVTLRADG-EREFMFYRNPSADMLLTADELNV 126 R L +R GVD VV + G RT F DG + ++R SA + + L+ Sbjct: 66 RYLLGEMRREGVDCSQVVCEPGERTGFQFKGRVDDGSDPPVEYHRRGSAASRMNPEHLDD 125 Query: 127 ELIKRAAVFHY-GSISLIAEPCRTAHLRAMEIAKEAGALLSYDPNLREALWPSREEARTQ 185 ++RA H G +AE + A +A+ + AG +S+DPNLR ALW + E R Sbjct: 126 RWLRRARHLHVTGVFPALAEGTQAATRQAIATMRAAGRTVSFDPNLRPALWATPELMRET 185 Query: 186 ILSIWDQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPT-MKLLLVTLGDQGCKYYARDF 244 + ++ Q D V E FLTG E + + +R +L++V LG +G + Sbjct: 186 LNNLAQQCDWVLPGIEEGRFLTG--HAEPERIAAFYRGRGARLVVVKLGAEGAYFDGEAG 243 Query: 245 HGAVPSFKVQQ-VDTTGAGDAFVGALLQRIVKDPSSLQDEKKLVESIKFANACGAITTTK 303 G VP+F V++ VDT GAGD F ++ S+L + + ++++ GA Sbjct: 244 TGHVPAFSVERVVDTVGAGDGFAVGVI-------SALLQGRTVADAVRRGAWIGARAVQV 296 Query: 304 KGAIPSLPTEA 314 +G LPT A Sbjct: 297 RGDTEGLPTHA 307 Lambda K H 0.319 0.136 0.388 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: 214 Number of extensions: 7 Number of successful extensions: 3 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: 323 Length of database: 314 Length adjustment: 27 Effective length of query: 296 Effective length of database: 287 Effective search space: 84952 Effective search space used: 84952 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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