Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_012976561.1 AZL_RS21475 gluconate kinase
Query= curated2:Q74BL5 (181 letters) >NCBI__GCF_000010725.1:WP_012976561.1 Length = 163 Score = 38.9 bits (89), Expect = 5e-08 Identities = 24/49 (48%), Positives = 32/49 (65%), Gaps = 6/49 (12%) Query: 16 VVLTGFMGTGKSTVGKLLARRLGYRFSDLDAL----IVE--RAGISINE 58 VV+ G G GK+TVG++LA RLG FSD D+ VE RAGI++ + Sbjct: 3 VVVMGVAGCGKTTVGQMLAARLGCGFSDADSFHPPANVEKMRAGIALGD 51 Lambda K H 0.318 0.135 0.369 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: 68 Number of extensions: 2 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: 181 Length of database: 163 Length adjustment: 18 Effective length of query: 163 Effective length of database: 145 Effective search space: 23635 Effective search space used: 23635 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