Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate 5208927 Shew_1428 fructokinase (RefSeq)
Query= SwissProt::P23917 (302 letters) >FitnessBrowser__PV4:5208927 Length = 296 Score = 388 bits (996), Expect = e-112 Identities = 182/299 (60%), Positives = 229/299 (76%), Gaps = 4/299 (1%) Query: 1 MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTV 60 MR+G+DLGGTK E++AL +AG++L+R R+PTPR+ Y+ T++ I LV+ AE GQ+GTV Sbjct: 2 MRMGVDLGGTKIELVALSEAGKELFRKRIPTPRE-YKATLDAIEALVNEAESTLGQKGTV 60 Query: 61 GMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAA 120 G+GIPG ISP++G+VKNANSTW+NG P D DL ARL+REVR+ANDANC AVSEAVDGAAA Sbjct: 61 GVGIPGVISPFSGLVKNANSTWINGHPLDLDLGARLEREVRVANDANCFAVSEAVDGAAA 120 Query: 121 GAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCGK 180 G VF VIIGTGCG G+A NG+ H GGNG GEWGHNPLPWM DE E C+CG Sbjct: 121 GKGLVFGVIIGTGCGGGIAINGKVHGGGNGIGGEWGHNPLPWMTPDEFNSTE---CFCGN 177 Query: 181 QGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHVV 240 + CIETFISGTGF DY+ G A G EI R +E+ + +A A RY RLA+SLAH++ Sbjct: 178 KDCIETFISGTGFVRDYKAAGGDAPSGIEIARRMEQGEALATAAFERYIDRLARSLAHMI 237 Query: 241 NILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAWLW 299 N+LDPD+IVLGGG+SN++ +Y + + + ++V GGEC TPV + +G SSGVRGAAWLW Sbjct: 238 NMLDPDIIVLGGGVSNIEAIYPRLPEALSKYVLGGECRTPVVQNMYGGSSGVRGAAWLW 296 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: 392 Number of extensions: 17 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: 302 Length of database: 296 Length adjustment: 27 Effective length of query: 275 Effective length of database: 269 Effective search space: 73975 Effective search space used: 73975 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