Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_017549879.1 C792_RS0112925 sugar kinase
Query= BRENDA::Q6VWJ5 (386 letters) >NCBI__GCF_000330705.1:WP_017549879.1 Length = 315 Score = 118 bits (295), Expect = 3e-31 Identities = 82/269 (30%), Positives = 133/269 (49%), Gaps = 8/269 (2%) Query: 68 VVCFGEMLIDFVPTTSGLSLAEAPAFKKAPGGAPANVAVGISRLGGSSAFIGKVGEDEFG 127 V+ GE ++ V G + A +FK GA N +G+SRLG ++++ +GEDE G Sbjct: 3 VIGIGESMVALVNEPKGY-IRHADSFKPYVAGAEMNTLIGLSRLGHGTSWVSALGEDELG 61 Query: 128 YMLAEILKENNVNSDGMRFDPGARTALAFVTLRKDGEREFMFYRNPSADMLLQEDELDLE 187 ++ ++ NV++ + RT + F + DG + +YR SA + ++D++ Sbjct: 62 ELILHKVRAENVDASHVTHKD-KRTGVFFKQILPDGSVDVTYYREDSAASNMDIRDIDMD 120 Query: 188 LIRKAKVFHYGSISL-ITEPCKSAHIAAAKAAKDAGVILSYDPNLRLPLWPSAESAREGI 246 IR+AKV + I+L ++ K A + A D V + +DPN+RL +W SA+ ARE I Sbjct: 121 AIRRAKVLYLTGITLSLSSSAKEMLFEAVRIAGD-DVTVVFDPNIRLKMW-SAKEARETI 178 Query: 247 LSIWNTADIIKISEEEISFLTQGEDPYDDNVVRKLYHPNLKLLLVTEGPEGCRYYTKDFS 306 L D + +E+ L P + ++ +++ G EG Y Sbjct: 179 LEFLPHVDCLIAGRDEVDILMGAMRP--EEALKSFRELGCSKVVLKLGKEGAVYDFDGIG 236 Query: 307 GRVKGIK-VDAVDTTGAGDAFVAGILSQL 334 G VK K + +D GAGDAF AGI+S L Sbjct: 237 GSVKNPKQFEEIDPVGAGDAFAAGIISGL 265 Lambda K H 0.317 0.134 0.382 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: 244 Number of extensions: 11 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: 386 Length of database: 315 Length adjustment: 29 Effective length of query: 357 Effective length of database: 286 Effective search space: 102102 Effective search space used: 102102 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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