Align Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized)
to candidate BPHYT_RS11300 BPHYT_RS11300 2-dehydro-3-deoxygluconokinase
Query= SwissProt::Q0JGZ6 (323 letters) >FitnessBrowser__BFirm:BPHYT_RS11300 Length = 327 Score = 115 bits (287), Expect = 2e-30 Identities = 98/323 (30%), Positives = 149/323 (46%), Gaps = 21/323 (6%) Query: 8 VVSFGEMLIDFVPTVAGVSLAEAPAFVKAPGGAPANVAIAVARLGGGAAFVGKLGDDEFG 67 V+++GE + FV G LA F K GA NVAI ++RLG ++ ++G+D FG Sbjct: 10 VITYGEAMAMFVAAETG-PLAGVGQFTKRVAGADLNVAIGLSRLGFKVGWMSRVGNDSFG 68 Query: 68 RMLAAILRDNGVDDGGVVFDAGARTALAFVTLRADG-EREFMFYRNPSADMLLTHAELNV 126 + + L G+D G V D T + DG + ++R SA L+ A+ Sbjct: 69 QYVRDTLTKEGIDQGCVTTDERYPTGFQLKSKNDDGSDPAIEYFRKGSAASHLSLADYAA 128 Query: 127 ELIKRAAVFHYGSISLIAEPCRSAHLR--AMEIAKE---AGALLSYDPNLREALWPSREE 181 + + +A H ++ P SA R A +A+E AG +S+DPNLR LWPSR Sbjct: 129 DYVLQARHLHLTGVA----PAISASSRELAFHLAREMRAAGKTISFDPNLRPTLWPSRAA 184 Query: 182 ARTKILSIWDQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPTMKLLLVTLGDQGCKYYA 241 + ++ AD V E E LTG + DD+ + +++ LG QG + Sbjct: 185 MVEGLNALAALADWVLPGIGEGEILTGY-TQPDDIAKFYLEQGARGVIIKLGAQGAYFRT 243 Query: 242 RDFRGAVPSYKVQQ-VDTTGAGDAFVGALLRRIVQDPSSLQDQKKLEEAIKFANACGAIT 300 D + V + VDT GAGD F ++ S+L + K L +A+ N GA+ Sbjct: 244 ADDAAMIAGQPVAKVVDTVGAGDGFAVGVV-------SALLEGKSLPQAVARGNRIGALA 296 Query: 301 ATKKGAIPSLPTEVEVLKLMESA 323 G LP+ E L +E+A Sbjct: 297 IQVIGDSEGLPSRAE-LDALEAA 318 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: 241 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: 327 Length adjustment: 28 Effective length of query: 295 Effective length of database: 299 Effective search space: 88205 Effective search space used: 88205 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