Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate Ga0059261_4061 Ga0059261_4061 Transcriptional regulator/sugar kinase
Query= reanno::Korea:Ga0059261_1776 (335 letters) >FitnessBrowser__Korea:Ga0059261_4061 Length = 291 Score = 190 bits (483), Expect = 3e-53 Identities = 118/293 (40%), Positives = 154/293 (52%), Gaps = 13/293 (4%) Query: 21 AVEAGGTKFLCGIADRTGSVLAQTRIPTTTPAETLDAATAFFAEHVARHGPLSAFSVGSF 80 A+E GGTK L + R V+A+ R PTT+P E +AA FA PL+ + +F Sbjct: 9 AIETGGTKLLARLV-RDEGVVAEARWPTTSP-EAAEAALLAFAGRT----PLAGVGIAAF 62 Query: 81 GPLSLDPIAPDYGSITSTPKPGWQDVDLLGYFRQMIDAPMALDTDVNCAAVGERLFGSGR 140 GP+ +DP A +YG + +TPKPGW +L Q + P+A+DTDVN AA+ E G+G+ Sbjct: 63 GPVVVDPAAANYGEVLATPKPGWTGANLRAALEQALGVPVAIDTDVNAAALAEAAAGAGQ 122 Query: 141 GLDTFCYVTVGTGIGVGLLVGGAPHGGANHPEAGHIRLPRAPGDHDFAGICPFHGDCLEG 200 G + YVTVGTGIG GL G GA HPE GH+ + R GD CPFH C EG Sbjct: 123 GCSSLAYVTVGTGIGAGLARDGRTLTGALHPEMGHVPVLRFEGD-PTPSACPFHSGCAEG 181 Query: 201 LACGPAMKARWGA-AAETLPGDHPAWDIEADYLAGLCATLTYIVRPDRIILGGGVMESHL 259 +A GPA++ R G E P D A ADYL L AT+ P RI++GGGVM+ Sbjct: 182 MAAGPAVQRRLGGKLLEDSPADFAA---VADYLGQLFATIVLAWSPHRIVVGGGVMDVPG 238 Query: 260 MHARVRRTLVAKLAGYDASMRSLDMDEYVVPPTAGPSAGLTGAFALAYRIVTR 312 + + L GY + D + A AGL GA LA + R Sbjct: 239 LGKAATVRMRVALGGYGVGSAVGEAD--FIRSAALEHAGLEGALILARQAAAR 289 Lambda K H 0.321 0.139 0.442 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: 309 Number of extensions: 23 Number of successful extensions: 5 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: 335 Length of database: 291 Length adjustment: 27 Effective length of query: 308 Effective length of database: 264 Effective search space: 81312 Effective search space used: 81312 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