Align Fructokinase-1; ZmFRK1; EC 2.7.1.4 (characterized)
to candidate WP_085771876.1 B1812_RS12430 adenosine kinase
Query= SwissProt::Q6XZ79 (323 letters) >NCBI__GCF_002117405.1:WP_085771876.1 Length = 333 Score = 61.6 bits (148), Expect = 3e-14 Identities = 70/237 (29%), Positives = 104/237 (43%), Gaps = 12/237 (5%) Query: 38 GGAPANVAIAVSRLGGGAAFVGKLGDDEFGRMLAAILRDNGVDDGGVVFDSGARTALAFV 97 GG+ AN ++ LG FVGK+ +DE GR A +R GV GA TA + Sbjct: 59 GGSAANTMAGLASLGCRVGFVGKVKEDEAGREFAHDIRKAGVAFETPFATDGAATARCLI 118 Query: 98 TLRADGEREFMFYRNPSADMLLTADELNVELIKRAAVFHYGSISLIAEPCRTAHLRAMEI 157 + DG+R + A L +++ A V + + A L+A ++ Sbjct: 119 FVTPDGQRTMNTFL--GACQALGPADIDEAQAADAKVLYLEGYLWDPPAAKEAFLKAAKL 176 Query: 158 AKEAGALLSYDPNLREALWPSREEARTQILS-IWDQ-ADIVKVSEVELEFLTGIDSVEDD 215 ++ G ++ +L +A R R + L I DQ DIV +E EL L + + D Sbjct: 177 SRAKGRKVAL--SLSDAFCVDR--YRDEFLGLIRDQLVDIVFANESELHSL--YQTADFD 230 Query: 216 VVMKLWRPTMKLL-LVTLGDQGCKYYARDFHGAVPSFKVQQ-VDTTGAGDAFVGALL 270 + R LL +VT QG +VP+F V++ VDTTGAGD F L Sbjct: 231 TALVALRAEKGLLGVVTRSAQGALVADAAGVVSVPAFAVEEIVDTTGAGDLFAAGFL 287 Lambda K H 0.319 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: 224 Number of extensions: 14 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: 333 Length adjustment: 28 Effective length of query: 295 Effective length of database: 305 Effective search space: 89975 Effective search space used: 89975 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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