Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_035254635.1 H567_RS0114935 shikimate kinase
Query= curated2:Q7NH27 (177 letters) >NCBI__GCF_000422285.1:WP_035254635.1 Length = 174 Score = 95.1 bits (235), Expect = 6e-25 Identities = 67/165 (40%), Positives = 94/165 (56%), Gaps = 7/165 (4%) Query: 6 SLYLVGMMGSGKSTVGRLLAEKLGYGFVDLDALIEQVSGKRVGEIFEREGEAVFRDLESR 65 ++ L+GM G+GKSTVG +LA+ GFVD D L++ G+ + EI ++EG R +E R Sbjct: 9 NIVLIGMPGAGKSTVGVILAKMAAMGFVDTDLLLQASEGRSLQEIVDQEGFMALRAIEER 68 Query: 66 VLAEVSAYTRLVVATGGGVVLARRNWGYLH-HGVVVWLDADIETLLGRVEHEPGTRPLLA 124 VL + V+ATGG V + G+L GVVV+LDA ETL R++ + TR + Sbjct: 69 VLLGLDLQGH-VIATGGSAVYSEAAMGHLKGAGVVVFLDAAAETLERRIQ-DFATRGIAR 126 Query: 125 GGDRHLRLVELLGERARLYAQ-ADVRVSAAGL-PPAVAEETLRCL 167 D+ EL GER LY + AD+R+ AGL AV +R L Sbjct: 127 RPDQ--SFAELYGERLALYHRYADIRIDCAGLTQEAVCARIIRAL 169 Lambda K H 0.320 0.139 0.401 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: 83 Number of extensions: 5 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: 177 Length of database: 174 Length adjustment: 19 Effective length of query: 158 Effective length of database: 155 Effective search space: 24490 Effective search space used: 24490 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: 44 (21.6 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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