Align Shikimate kinase 2; SK 2; EC 2.7.1.71 (uncharacterized)
to candidate WP_008807483.1 KVAR_RS21655 adenylyl-sulfate kinase
Query= curated2:Q2NVB6 (174 letters) >NCBI__GCF_000025465.1:WP_008807483.1 Length = 176 Score = 42.4 bits (98), Expect = 4e-09 Identities = 28/90 (31%), Positives = 47/90 (52%), Gaps = 6/90 (6%) Query: 3 QHLFMVGARGCGKTTVGQALARVLGYAFADTDDMLWRS--TGKTVAEIVAKEGWTGFRAR 60 Q + ++G G GK+TVGQALA LG F D DD+ R+ ++ + E + R Sbjct: 4 QCIILMGVSGTGKSTVGQALAHALGAKFIDGDDLHPRNNIVKMATSQPLNDEDRQPWLTR 63 Query: 61 ESEILTSVTQGNAVVATGGGIILSAANRRF 90 ++++ S+ Q N G ++ SA +R+ Sbjct: 64 IADVIFSLEQKN----ESGVLVCSALKKRY 89 Lambda K H 0.318 0.130 0.373 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: 72 Number of extensions: 6 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: 174 Length of database: 176 Length adjustment: 19 Effective length of query: 155 Effective length of database: 157 Effective search space: 24335 Effective search space used: 24335 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