Align Fructokinase; EC 2.7.1.4 (uncharacterized)
to candidate Echvi_0156 Echvi_0156 Sugar kinases, ribokinase family
Query= curated2:P22824 (307 letters) >FitnessBrowser__Cola:Echvi_0156 Length = 314 Score = 79.7 bits (195), Expect = 8e-20 Identities = 80/273 (29%), Positives = 119/273 (43%), Gaps = 23/273 (8%) Query: 27 GGAPANVAVAIARLSGKSAFFGRVGDDPFGRFMQSILDQEGVCTEFLIKDPEQRTSTVVV 86 G + A A IA L +AF G VG D FG+ +Q L + V T F+ + +T VV Sbjct: 41 GSSSAIFAANIATLGVDTAFCGMVGKDDFGKMVQETLAAQQVDTRFIATSAQYKTGLTVV 100 Query: 87 DLDDQGERSFTFMVKPSADQFMSV--EDMGNFKQGDWLHVCSISLANEPSRSSTFEAIKR 144 DQ + T+ A + E G FK H+ + L + T ++ Sbjct: 101 MNYDQDRANVTYCGAMEALTMQEIPWEVAGTFKH---FHLSNYFLQKGIQKDIT-AIFEK 156 Query: 145 AKAAGGFISFDPNL-RDEVWQDQSEIQAVVMKAVAMADVVKFSEEELLFLTDSTSMAQGL 203 AK+AG S D + D+ W E + + D+ +E ELL LT +S+++ L Sbjct: 157 AKSAGMTTSLDLQVDPDDQWDFDYE------RCLPHVDIFLPNESELLSLTGKSSISEAL 210 Query: 204 QQIAAMNIALVLVTQGAKGVWRVFESQSELITGQVVSP--IDTTGAGDAFVGGLLACLSR 261 + I V + +G KG VFE V+ +D GAGD+F G + + Sbjct: 211 EAIKPY-ANTVALKRGVKG-GLVFEKGKVTEVAAFVNDQFVDAIGAGDSFNAGFIHRFLQ 268 Query: 262 HADWKNHPVVSSAIQWANGCGALATTQKGAMTA 294 ADW+ S +++AN GAL TT G A Sbjct: 269 GADWE------SCLRFANLTGALNTTAAGGTGA 295 Lambda K H 0.318 0.132 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: 228 Number of extensions: 15 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: 307 Length of database: 314 Length adjustment: 27 Effective length of query: 280 Effective length of database: 287 Effective search space: 80360 Effective search space used: 80360 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 (21.8 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