Align Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized)
to candidate 3608582 Dshi_1976 PfkB domain protein (RefSeq)
Query= SwissProt::A2WXV8 (323 letters) >FitnessBrowser__Dino:3608582 Length = 305 Score = 94.7 bits (234), Expect = 2e-24 Identities = 94/297 (31%), Positives = 143/297 (48%), Gaps = 33/297 (11%) Query: 32 AFVKAPGGAPANVAIAVARLGGGAAFVGKLGDDEFGRMLAAILRDNGVDDGGVVFDAGAR 91 +F PGG +N AIA A+ GG A F+ +LG+D F M AAI + GV D + Sbjct: 33 SFALNPGGKGSNQAIAAAKSGGDARFLTRLGEDAFADMAAAIWAEAGV-RATAPRDPASY 91 Query: 92 TALAFVTL-RADGEREFMFYRNPSADMLLTHAELN--VELIKRAAVFHYGSISLIAEPCR 148 T A++ + A G+ + P A LL A+L+ E+I A VF ++ + +P Sbjct: 92 TGAAYIYVDPATGDNAIIV--APGAAALLGPADLDAQAEMIGGAGVF----LTQLEQPMP 145 Query: 149 SAHLRAMEIAKEAGALLSYDPNLREALWPSREEARTKILSIWDHADIVKVSEVELEFLTG 208 +A R +EIA+ AG +P L ++A + DIV +E E E LTG Sbjct: 146 AAR-RGLEIARAAGVTTILNPAPAAPL----DDALLAL------CDIVTPNETEAEALTG 194 Query: 209 IDSVEDDVVMK----LWRPTMKLLLVTLGDQGCKYYARDFRGAVPSYKV-QQVDTTGAGD 263 D ++ L ++VTLG QG Y + P++ V+TTGAGD Sbjct: 195 HPVTGPDDAVRAADALLARGPGAVIVTLGAQGVLYRSATQTIHQPAFTPGPVVETTGAGD 254 Query: 264 AFVGALLRRIVQDPSSLQDQKKLEEAIKFANACGAITATKKGAIPSLPTEVEVLKLM 320 AF GAL ++L + + A++F A +I+ T+ GA PS+P+ E+ L+ Sbjct: 255 AFNGAL-------ATALAEGQDTASALRFGCATASISVTRPGAGPSMPSRAEIDALL 304 Lambda K H 0.320 0.136 0.389 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: 237 Number of extensions: 8 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: 323 Length of database: 305 Length adjustment: 27 Effective length of query: 296 Effective length of database: 278 Effective search space: 82288 Effective search space used: 82288 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 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