Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate WP_011840150.1 RSPH17029_RS00375 ROK family protein
Query= SwissProt::P23917 (302 letters) >NCBI__GCF_000015985.1:WP_011840150.1 Length = 295 Score = 139 bits (349), Expect = 1e-37 Identities = 96/300 (32%), Positives = 150/300 (50%), Gaps = 17/300 (5%) Query: 1 MRIGIDLGGTKTEVIAL--GDAGEQLYRHRLPTPRDDYRQTIETIATLVD-MAEQATGQR 57 M I D+GG++ D E L +P + +A L D M E+AT Sbjct: 1 MLIAFDIGGSRIRAARAFAPDDLEPLGERPMPLSFPGF------VAALRDLMPEEAT--- 51 Query: 58 GTVGMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDG 117 ++ + I G + P TG + AN +N + DL A L R V + NDA+C ++EA+ G Sbjct: 52 -SLAIAIAGVVDPDTGRITAANLPAVNQRALAADLCAALGRPVWIGNDADCFVLTEALLG 110 Query: 118 AAAGAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDEL-RYREEVPC 176 G ++VF +I+G+G G G+ +GR G G AGEWGH P+ +D+ L R +PC Sbjct: 111 VGRGHRSVFGIILGSGVGGGIVLDGRLLTGAGGIAGEWGHAPV--LDQRPLGRDLPHLPC 168 Query: 177 YCGKQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSL 236 CG+ GC++T+ S G + L G L EI+ + A + + +A L Sbjct: 169 GCGQSGCVDTYGSARGIERLHLALCGQRLDSREILAAWRAGEMAAAETVEVWLELVAGPL 228 Query: 237 AHVVNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAA 296 A +VN++ P V+ +GGG+SN L + + ++ + ET +R A H + G+ GAA Sbjct: 229 AMLVNVIGPSVVPVGGGLSNDGDLVAALDRAVRHRLLRPASETLLRPAFHPE-PGLVGAA 287 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: 279 Number of extensions: 12 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: 295 Length adjustment: 27 Effective length of query: 275 Effective length of database: 268 Effective search space: 73700 Effective search space used: 73700 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 Apr 10 2024. 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