Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_084456376.1 G494_RS0104115 shikimate kinase
Query= curated2:Q2LUD6 (195 letters) >NCBI__GCF_000429965.1:WP_084456376.1 Length = 199 Score = 110 bits (274), Expect = 2e-29 Identities = 69/184 (37%), Positives = 98/184 (53%), Gaps = 8/184 (4%) Query: 8 ENDDRNIILIGYRGTGKTSVGQELARRLHRPFHDTDVLIEKREGRSIRDMVAREGWAFFR 67 E +I+L G+R TGK+ VG LA RL D+D I +R G ++ ++VA+ GW FR Sbjct: 21 EKKQTSILLTGFRATGKSVVGALLAERLGFQLVDSDQEICRRRGMTVAEIVAQSGWEGFR 80 Query: 68 ERERAAISSLDGLRRCVLATGGGAVLDPKNAEVLKSLGWVVLLTASEEIIVRRILNDPAS 127 E+ + L R VLA GGGA+ + L+ WVV L A IV+R+ +D AS Sbjct: 81 RAEQELLLELCDAERVVLAVGGGAIEHQELWPQLRQSYWVVWLRADVATIVQRMGDDHAS 140 Query: 128 REQRPSFSGKASTEISEETMRKETTEILKQRMPIYRVLADQIIDTSQISTAEIVDEILRR 187 QRPS +G E E +L +R P+YR +D +DT Q A++V+EI+ R Sbjct: 141 SGQRPSLTGLGRAE--------EVAALLTRRTPLYRDGSDLALDTDQSRPAQLVEEIIAR 192 Query: 188 FQSQ 191 Q Sbjct: 193 LGLQ 196 Lambda K H 0.320 0.135 0.374 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: 108 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: 195 Length of database: 199 Length adjustment: 20 Effective length of query: 175 Effective length of database: 179 Effective search space: 31325 Effective search space used: 31325 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: 45 (21.9 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