Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate WP_044176839.1 ACIX8_RS15175 fructokinase
Query= SwissProt::P23917 (302 letters) >NCBI__GCF_000178955.2:WP_044176839.1 Length = 301 Score = 363 bits (932), Expect = e-105 Identities = 181/302 (59%), Positives = 220/302 (72%), Gaps = 3/302 (0%) Query: 1 MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTV 60 MRIGIDLGGTK E IAL G++L R R+ TPR DY T+ TIA LV EQAT + G+V Sbjct: 1 MRIGIDLGGTKIEAIALDAKGQELRRIRVATPRGDYDATVSTIAGLVHDMEQATKRVGSV 60 Query: 61 GMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAA 120 G+GIPG+I TG+VKNANSTW+NG+PF DLS L+REVR ANDANC AVSEA DGAA Sbjct: 61 GVGIPGTIIESTGLVKNANSTWINGRPFQHDLSVALEREVRCANDANCFAVSEATDGAAR 120 Query: 121 GAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCGK 180 GA+ VF VI+GTGCG GVA +GR H G NG AGEWGH PLPW DE+ + CYCG+ Sbjct: 121 GARIVFGVIVGTGCGGGVAIDGRVHAGRNGIAGEWGHIPLPWAQGDEVPGPQ---CYCGR 177 Query: 181 QGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHVV 240 GC+ET+ISGTGF D+ R +G L G EI+ E D A AL R E R+A+ LA ++ Sbjct: 178 TGCLETWISGTGFEQDFARRTGRDLLGKEIVAAAEAGDAEALDALDRLEDRMARGLAIMI 237 Query: 241 NILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAWLWP 300 +ILDPDVIV+GGG+SN++RLY + + ++ + FGG +TPV +A HGDSSGVRGAAWLW Sbjct: 238 DILDPDVIVMGGGLSNIERLYAGISRRLRDYPFGGGVDTPVVRAVHGDSSGVRGAAWLWQ 297 Query: 301 QE 302 E Sbjct: 298 PE 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: 361 Number of extensions: 16 Number of successful extensions: 2 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: 301 Length adjustment: 27 Effective length of query: 275 Effective length of database: 274 Effective search space: 75350 Effective search space used: 75350 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 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