Align Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized)
to candidate WP_007680610.1 BN137_RS02010 sugar kinase
Query= SwissProt::Q0JGZ6 (323 letters) >NCBI__GCF_000319285.1:WP_007680610.1 Length = 312 Score = 113 bits (282), Expect = 7e-30 Identities = 94/312 (30%), Positives = 133/312 (42%), Gaps = 11/312 (3%) Query: 8 VVSFGEMLIDFVPTVAGVSLAEAPAFVKAPGGAPANVAIAVARLGGGAAFVGKLGDDEFG 67 V++ GE + FV T G LA+ F K GA NVA +ARLG ++V ++G+D FG Sbjct: 7 VITIGEAMAMFVATEPG-DLAQVEHFFKRVAGAELNVATGLARLGLNVSWVSRVGNDSFG 65 Query: 68 RMLAAILRDNGVDDGGVVFDAGARTALAFVTLRADG-EREFMFYRNPSADMLLTHAELNV 126 R + + L G+ GV D T + DG + ++R SA L+ + N Sbjct: 66 RFVLSQLEKEGISTRGVTIDDRFPTGFQLKSKVTDGTDPSVEYFRKGSAASHLSGEDFNA 125 Query: 127 ELIKRAAVFHYGSISLIAEPCRSAHL-RAMEIAKEAGALLSYDPNLREALWPSREEARTK 185 L A H ++ L A K G +S+DPNLR LW S E K Sbjct: 126 PLFYSARHLHLSGVAAALSGSSYELLDHAARAMKTQGKTISFDPNLRPVLWKSEAEMVEK 185 Query: 186 ILSIWDQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPTMKLLLVTLGDQGCKYYARDFR 245 + + AD V E LTG E L R +++ T D A + Sbjct: 186 LNHLATLADWVLPGLKEGHILTGQQHPEGIADFYLSRGVKAVVIKTGADGAWYQTASGEQ 245 Query: 246 GAVPSYKVQQ-VDTTGAGDAFVGALLRRIVQDPSSLQDQKKLEEAIKFANACGAITATKK 304 G V + KV VDT GAGD F ++ S+L + K L +A N GA+ + Sbjct: 246 GTVEAVKVDNVVDTVGAGDGFAVGVI-------SALLEGKTLHQAATRGNKIGALAIQVQ 298 Query: 305 GAIPSLPTEVEV 316 G LPT ++ Sbjct: 299 GDSEGLPTRAQL 310 Lambda K H 0.320 0.136 0.388 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: 221 Number of extensions: 9 Number of successful extensions: 4 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: 323 Length of database: 312 Length adjustment: 27 Effective length of query: 296 Effective length of database: 285 Effective search space: 84360 Effective search space used: 84360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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