Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate WP_040480287.1 C943_RS09665 ROK family protein
Query= SwissProt::P23917 (302 letters) >NCBI__GCF_000330725.2:WP_040480287.1 Length = 294 Score = 85.9 bits (211), Expect = 1e-21 Identities = 77/255 (30%), Positives = 113/255 (44%), Gaps = 32/255 (12%) Query: 3 IGIDLGGTKTEVIALGDAGEQLYRHRL-PTPRDDYRQTI-ETIATLVDMAEQATGQRGTV 60 +G+D+GGT + L G +L R+ TP + ++ I ETIA L+ + Sbjct: 9 LGLDIGGTNIKAGVL--VGSELVDIRMIETPSQESQEYILETIADLI--GTYLHHDFFAI 64 Query: 61 GMGIPGSISPYTGVVKNA-NSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAA 119 G+GIPG I G+V N N + L R + V + NDANC A+ E GAA Sbjct: 65 GVGIPGLIDTDLGIVLNLENIPSFKRVHLREFLELRFGKPVYINNDANCFALGEYKFGAA 124 Query: 120 AGAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCG 179 + V + +GTG GAG+ NG + G N AGEW P++D+D Sbjct: 125 KIYKHVVGITLGTGLGAGIIANGHLYCGFNCAAGEW--CSAPYLDQD------------- 169 Query: 180 KQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHV 239 E + S F Y HA K + + ++ D A A Y L + + ++ Sbjct: 170 ----FEFYCSSKFFYAKY-----HA-KAKSLSKRAKDGDKEALRAYAEYGHHLGELIKNI 219 Query: 240 VNILDPDVIVLGGGM 254 + L P IVLGG + Sbjct: 220 LYTLAPQAIVLGGSI 234 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: 250 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: 294 Length adjustment: 26 Effective length of query: 276 Effective length of database: 268 Effective search space: 73968 Effective search space used: 73968 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