Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate 15241 b1119 N-acetyl-D-glucosamine kinase (NCBI)
Query= SwissProt::P23917 (302 letters) >FitnessBrowser__Keio:15241 Length = 303 Score = 206 bits (524), Expect = 5e-58 Identities = 124/306 (40%), Positives = 173/306 (56%), Gaps = 15/306 (4%) Query: 1 MRIGIDLGGTKTEVIALG--DAGEQL-YRHRLPTPRDDYRQTIETIATLVDMAEQATGQR 57 M G D+GGTK IALG D+G QL + R+PTPRD Y ++ + LV A+Q G + Sbjct: 1 MYYGFDIGGTK---IALGVFDSGRQLQWEKRVPTPRDSYDAFLDAVCELVAEADQRFGCK 57 Query: 58 GTVGMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDG 117 G+VG+GIPG G + AN +G+P DLSARL R+VRL NDANC A+SEA D Sbjct: 58 GSVGIGIPGMPETEDGTLYAANVPAASGKPLRADLSARLDRDVRLDNDANCFALSEAWDD 117 Query: 118 AAAGAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLP-----WMDEDELRYRE 172 V +I+GTG G G+ FNG+ G + GE+GH LP M D R Sbjct: 118 EFTQYPLVMGLILGTGVGGGLIFNGKPITGKSYITGEFGHMRLPVDALTMMGLDFPLRR- 176 Query: 173 EVPCYCGKQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRL 232 C CG+ GCIE ++SG GFA Y+ L+ EII L ++ D A + RY L Sbjct: 177 ---CGCGQHGCIENYLSGRGFAWLYQHYYHQPLQAPEIIALYDQGDEQARAHVERYLDLL 233 Query: 233 AKSLAHVVNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGV 292 A L +++ I+DPD++V+GGG+SN + + + + + + +A+HGD+ G+ Sbjct: 234 AVCLGNILTIVDPDLVVIGGGLSNFPAITTQLADRLPRHLLPVARVPRIERARHGDAGGM 293 Query: 293 RGAAWL 298 RGAA+L Sbjct: 294 RGAAFL 299 Lambda K H 0.318 0.137 0.418 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: 306 Number of extensions: 13 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: 302 Length of database: 303 Length adjustment: 27 Effective length of query: 275 Effective length of database: 276 Effective search space: 75900 Effective search space used: 75900 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: 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