Align Fructokinase-2; Fructokinase II; OsFKII; EC 2.7.1.4 (characterized)
to candidate WP_011317140.1 AVA_RS01255 ribokinase
Query= SwissProt::A2YQL4 (336 letters) >NCBI__GCF_000204075.1:WP_011317140.1 Length = 307 Score = 100 bits (249), Expect = 5e-26 Identities = 97/314 (30%), Positives = 144/314 (45%), Gaps = 33/314 (10%) Query: 19 VVSFGEMLIDFVPD-----VAGVSLAESGGFVKAPGGAPANVACAISKLGGSSAFVGKFG 73 ++ FG + ID V +AG +L F K PGG AN A A++KLG + VG+ G Sbjct: 3 IIVFGSINIDLVATAPKLPIAGETLLGED-FFKVPGGKGANQAVAVAKLGVPTQMVGRVG 61 Query: 74 DDEFGHMLVDILKKNGVNAEGCLFDEHARTALAFVTLKSNGEREFMFYRNPSADMLLTEA 133 FG L++ L+ GV + DE A + +A +T+ +GE + + P A+ + +A Sbjct: 62 AHGFGAELMENLQDAGVQTDNIFVDETASSGVAMITVAHDGENQIVVI--PGANGRVNQA 119 Query: 134 ELNLDLIRRAKIFHYGSISLI-TEPCRSAHVAAMRAAKSAGILCSYDPNVRLPLWPSEDA 192 D+ R + I + L+ E +A +AA +AA+S I DP P+E Sbjct: 120 ----DVERLSYILPTATALLLQLEIPITAVIAAAQAARSNNITVILDPAPAPSDLPAE-- 173 Query: 193 ARAGILSIWKEADFIKVSDDE----VAFLTQGDANDEKNVLSLWFDGLKLLIVTDGEKGC 248 ++ D I ++ E V F G+ K L G+K IV G KG Sbjct: 174 -------LYPLIDIITPNEVEAGQIVGFPVDGEEAARKAAGVLLQRGVKSAIVKLGAKGV 226 Query: 249 RYFTKDFKGSVPGFSVNTVDTTGAGDAFVGSLLVNVAKDDSIFHNEEKLREALKFSNACG 308 T VP F V+TVDT AGDAF G L + ++ L +A+ + A G Sbjct: 227 VCATDKETFFVPAFFVDTVDTVAAGDAFNGGLA-------TALYSGLSLHQAVIWGAAAG 279 Query: 309 AICTTKKGAIPALP 322 A+ TK GA +LP Sbjct: 280 ALAATKLGAQTSLP 293 Lambda K H 0.319 0.135 0.396 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: 224 Number of extensions: 10 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: 336 Length of database: 307 Length adjustment: 28 Effective length of query: 308 Effective length of database: 279 Effective search space: 85932 Effective search space used: 85932 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 (21.7 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