Align shikimate kinase (EC 2.7.1.71) (characterized)
to candidate WP_026127895.1 D471_RS0120015 shikimate kinase
Query= BRENDA::P9WPY3 (176 letters) >NCBI__GCF_000341125.1:WP_026127895.1 Length = 171 Score = 143 bits (360), Expect = 2e-39 Identities = 77/161 (47%), Positives = 102/161 (63%), Gaps = 1/161 (0%) Query: 6 VLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEEDVV 65 +L+G PGSGKST+GR LA+ LG LL TD IE+R G+ I DIF DGE FR +E +VV Sbjct: 1 MLIGSPGSGKSTVGRALAERLGAELLCTDTEIEKRAGKPIGDIFVEDGEPHFRALEREVV 60 Query: 66 RAALADHDGVLSLGGGAVTSPGVRAALAGHTVVYLEISAAEGVRRTGGNTVRPLLAGPDR 125 L +GV+++GGGAV RA LA H VVYL++ AE +R G + RPLLAG R Sbjct: 61 AEGLRSWEGVIAVGGGAVLDEDTRADLADHHVVYLQVEFAEAAKRVGMDVARPLLAGNPR 120 Query: 126 AEKYRALMAKRAPLYRRVATMRVDTNRRNPGAVVRHILSRL 166 + R L+ +R P+Y +AT+ V T ++P +V IL L Sbjct: 121 T-RLRKLLDERLPIYEGLATVTVPTTDQHPEEIVDAILPTL 160 Lambda K H 0.318 0.134 0.375 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: 126 Number of extensions: 5 Number of successful extensions: 1 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: 176 Length of database: 171 Length adjustment: 19 Effective length of query: 157 Effective length of database: 152 Effective search space: 23864 Effective search space used: 23864 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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