Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate 200821 SO1656 ROK family protein (NCBI ptt file)
Query= SwissProt::P23917 (302 letters) >FitnessBrowser__MR1:200821 Length = 306 Score = 359 bits (922), Expect = e-104 Identities = 179/307 (58%), Positives = 216/307 (70%), Gaps = 12/307 (3%) Query: 1 MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTV 60 +R+GIDLGGTK E++AL + G ++ R R+ TPRD Y+ T+ I LV+ AE G++G+V Sbjct: 2 IRMGIDLGGTKIELVALNNEGNEVVRKRINTPRD-YQGTLNAIVDLVNEAESTLGEKGSV 60 Query: 61 GMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAA 120 G+GIPG ISPY+G+VKNANSTW+NG P D L L REVR+ANDANC A+SEAVDGAAA Sbjct: 61 GVGIPGVISPYSGLVKNANSTWINGHPLDVHLGELLGREVRVANDANCFALSEAVDGAAA 120 Query: 121 GAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCGK 180 G VF VIIGTGCGAGVA NG+ H GGNG GEWGHNPLPWM ++E C+CG Sbjct: 121 GKSVVFGVIIGTGCGAGVAINGKVHAGGNGIGGEWGHNPLPWMTKEEF---NTTRCFCGN 177 Query: 181 QGCIETFISGTGFAMDYRRLSGHAL--------KGSEIIRLVEESDPVAELALRRYELRL 232 CIETFISGTGF DY A GSEI+ LV+ D +A A RY RL Sbjct: 178 PDCIETFISGTGFVRDYNEALSRAASVQRVPAKSGSEIMSLVDGGDEIALAAFERYVDRL 237 Query: 233 AKSLAHVVNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGV 292 A+SLAHV+N+LDPD IVLGGGMSNV+ +Y + L+ +V G EC TPV + +G SSGV Sbjct: 238 ARSLAHVINLLDPDAIVLGGGMSNVEAIYPRLPALLSHYVVGRECRTPVVQNLYGCSSGV 297 Query: 293 RGAAWLW 299 RGAAWLW Sbjct: 298 RGAAWLW 304 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: 365 Number of extensions: 18 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: 306 Length adjustment: 27 Effective length of query: 275 Effective length of database: 279 Effective search space: 76725 Effective search space used: 76725 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