Align Fructokinase-1; ZmFRK1; EC 2.7.1.4 (characterized)
to candidate WP_027699314.1 TT13_RS06945 ribokinase
Query= SwissProt::Q6XZ79 (323 letters) >NCBI__GCF_000691805.2:WP_027699314.1 Length = 306 Score = 120 bits (302), Expect = 3e-32 Identities = 92/287 (32%), Positives = 139/287 (48%), Gaps = 26/287 (9%) Query: 38 GGAPANVAIAVSRLGGGAAFVGKLGDDEFGRMLAAILRDNGVDDGGVVFDSGARTALAFV 97 GG AN A+A +R GG +FVG +G DE G +LR+ G+D G+V T A + Sbjct: 38 GGKGANQAVAAARQGGQVSFVGAVGADEAGERFKKVLREEGIDVSGIVTKK-VPTGSASI 96 Query: 98 TLRADGEREFMFYRNPSADMLLTADELNVELIKRAAVFHYGSISLIA-EPCRTAHLRAME 156 L DG M Y +A+ LTAD++ +K + + + E + A +A Sbjct: 97 LLEDDGHNTIMVYGGANAE--LTADDI----VKSENIIANADVVIAQFEVPQEAVAKAFY 150 Query: 157 IAKEAGALLSYDPNLREALWPSREEARTQILSIWDQADIVKVSEVELEFLTGIDSVEDDV 216 AK+ GAL +P A +E ++LS DI+ +E E L G++ D Sbjct: 151 FAKKYGALTILNP----APIIEQEAILPEVLS---STDIIVPNETEAAALVGMEPSTDKA 203 Query: 217 VMKLWRPTMKLL-----LVTLGDQGCKYYARDFHGAVPSFKVQQVDTTGAGDAFVGALLQ 271 + R M L ++TLG+ G Y+ D P FKV+ VDTT AGD F+G+L Sbjct: 204 KLAAVREAMAQLTIQKTVITLGEDGVFYHLADEDQVAPIFKVKPVDTTAAGDTFIGSLTV 263 Query: 272 RIVKDPSSLQDEKKLVESIKFANACGAITTTKKGAIPSLPTEAEVLQ 318 + KD ++ E+IK+++ +I GA+ S+PT EVL+ Sbjct: 264 ELNKDLTN------AAEAIKYSSKASSIAIQHFGALQSIPTRREVLK 304 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: 222 Number of extensions: 11 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: 323 Length of database: 306 Length adjustment: 27 Effective length of query: 296 Effective length of database: 279 Effective search space: 82584 Effective search space used: 82584 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 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