Align Fructokinase-1; ZmFRK1; EC 2.7.1.4 (characterized)
to candidate Ac3H11_1839 Ribokinase (EC 2.7.1.15)
Query= SwissProt::Q6XZ79 (323 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1839 Length = 314 Score = 96.7 bits (239), Expect = 7e-25 Identities = 87/297 (29%), Positives = 127/297 (42%), Gaps = 39/297 (13%) Query: 30 APAFLKAPGGAPANVAIAVSRLGGGAAFVGKLGDDEFGRMLAAILRDNGVDDGGVVFDSG 89 A A PGG N A+A +R G A G++GDD +G L A L +G+D GV D+ Sbjct: 35 ADALHLVPGGKGGNQAVACARQGAQVALFGRVGDDGYGHTLRAGLDADGIDHSGVQTDTA 94 Query: 90 ARTALAFVTLRADGEREFMFYRNPSADMLLTADELNVELIKRAAVFHYGSISLIAEPCRT 149 T +A +T+ A G+ + + +L A L AA+ G + L E Sbjct: 95 TTTGVAAITVEATGQNRIVVVPGANGRFVLDATALG------AALQGAGGLVLQFETPLR 148 Query: 150 AHLRAMEIAKEAGALLSYDPN----LREALWPSREEARTQILSIWDQADIVKVSEVELEF 205 L A E+A AG + +P+ L EALWP + V+EVE Sbjct: 149 QVLAAAEMAHAAGCPVVLNPSPIQPLPEALWP--------------LVHTLVVNEVEAAA 194 Query: 206 LTG------IDSVEDDVVMKLWRPTMKLLLVTLGDQGCKYYARDFHGAVPSFKVQQVDTT 259 L G D+ + ++ P ++VTLG G + P V+ VDTT Sbjct: 195 LAGQNVTTPADAAQAAQALRAKGPAQ--VVVTLGAAGAVAADAAGNRYHPGLVVRAVDTT 252 Query: 260 GAGDAFVGALLQRIVKDPSSLQDEKKLVESIKFANACGAITTTKKGAIPSLPTEAEV 316 AGD F+GAL + + + L ++ A+ T+ GA PS+PT A V Sbjct: 253 AAGDTFLGALAVALARG-------EPLDAGVREGIRAAALCVTQHGAQPSIPTRAAV 302 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: 225 Number of extensions: 14 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: 314 Length adjustment: 27 Effective length of query: 296 Effective length of database: 287 Effective search space: 84952 Effective search space used: 84952 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