Align Fructokinase-1; ZmFRK1; EC 2.7.1.4 (characterized)
to candidate 17812 b3752 ribokinase (NCBI)
Query= SwissProt::Q6XZ79 (323 letters) >FitnessBrowser__Keio:17812 Length = 309 Score = 111 bits (277), Expect = 3e-29 Identities = 87/289 (30%), Positives = 137/289 (47%), Gaps = 26/289 (8%) Query: 38 GGAPANVAIAVSRLGGGAAFVGKLGDDEFGRMLAAILRDNGVDDGGVVFDSGARTALAFV 97 GG AN A+A R G AF+ GDD G + L + +D V G T +A + Sbjct: 41 GGKGANQAVAAGRSGANIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALI 100 Query: 98 TLRADGEREFMFYRNPSADMLLTADELNVELIKRAAVFHYGSISLIAEPCRTAHLRAMEI 157 + +GE + +A + E E I A+ + + P + + A +I Sbjct: 101 FVNGEGENVIGIHAGANAALSPALVEAQRERIANASAL----LMQLESPLESV-MAAAKI 155 Query: 158 AKEAGALLSYDPNLREALWPSREEARTQILSIWDQADIVKVSEVELEFLTGIDSVEDDVV 217 A + +++ +P P+R E ++L++ DI+ +E E E LTGI D+ Sbjct: 156 AHQNKTIVALNPA------PAR-ELPDELLAL---VDIITPNETEAEKLTGIRVENDEDA 205 Query: 218 MK----LWRPTMKLLLVTLGDQGCKYYARDFHGAVPSFKVQQVDTTGAGDAFVGALLQRI 273 K L ++ +L+TLG +G VP F+VQ VDT AGD F GAL+ Sbjct: 206 AKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGFRVQAVDTIAAGDTFNGALI--- 262 Query: 274 VKDPSSLQDEKKLVESIKFANACGAITTTKKGAIPSLPTEAEVLQLIEK 322 ++L +EK L E+I+FA+A AI T+KGA PS+P E+ +++ Sbjct: 263 ----TALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDAFLDR 307 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: 217 Number of extensions: 13 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: 309 Length adjustment: 27 Effective length of query: 296 Effective length of database: 282 Effective search space: 83472 Effective search space used: 83472 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