Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate CCNA_02549 CCNA_02549 glucokinase
Query= SwissProt::P23917 (302 letters) >FitnessBrowser__Caulo:CCNA_02549 Length = 296 Score = 311 bits (797), Expect = 1e-89 Identities = 165/303 (54%), Positives = 206/303 (67%), Gaps = 10/303 (3%) Query: 1 MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQ-ATGQRGT 59 +R G+D GGTK EV AL AG+ + R R P P +Y + +E +A LV AE A G Sbjct: 2 IRFGVDFGGTKIEVAALNAAGDFVARVRKPNP-GNYDEALEVVAALVADAESMAGGSCAR 60 Query: 60 VGMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAA 119 +G+GIPGSISP TG+++NANST+LNG+PF ++L RL R VR+ANDANCLA+SEA DGA Sbjct: 61 LGLGIPGSISPRTGLIRNANSTYLNGRPFGENLETRLARPVRIANDANCLALSEAADGAG 120 Query: 120 AGAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCG 179 AGA VFA I+GTGCG GV +G+ G NG GEWGH PLPW +E + C+CG Sbjct: 121 AGASVVFAAIVGTGCGGGVVVDGKIINGHNGIGGEWGHAPLPWPKPEEYPGPD---CWCG 177 Query: 180 KQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHV 239 ++GC+ET+I+G FA D +G A G ++ + E D A AL RY RLA+SLA V Sbjct: 178 RKGCLETWIAGPAFARD----AGFA-NGQAAMQAIGEGDVKASAALDRYVDRLARSLAVV 232 Query: 240 VNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAWLW 299 +++DPD+IVLGGGMSNVD LY+ + I VF ETPVRKA HGDSSGVRGA WLW Sbjct: 233 CDLIDPDIIVLGGGMSNVDALYERLPAAIAPHVFSDIFETPVRKAVHGDSSGVRGAVWLW 292 Query: 300 PQE 302 P E Sbjct: 293 PPE 295 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: 327 Number of extensions: 19 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