Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_012506069.1 PAES_RS07580 shikimate kinase
Query= curated2:B3QMM3 (187 letters) >NCBI__GCF_000020625.1:WP_012506069.1 Length = 197 Score = 249 bits (635), Expect = 3e-71 Identities = 119/185 (64%), Positives = 156/185 (84%) Query: 1 MKHHSLIFLTGFSGSGKSTIGPLLANSLGFEFIDLDREIELAAGKSINRIFAEDGEAAFR 60 MK SLI+LTGFSGSGKSTIGPLLANSLG++F+DLD++IE AGK+INRIF E+GEA FR Sbjct: 1 MKQPSLIYLTGFSGSGKSTIGPLLANSLGYDFVDLDQQIEHLAGKTINRIFTEEGEAHFR 60 Query: 61 ELELRTLERIGSQKEMVVSLGGGVLENDRCFELIRRTGTLVYMKSSPEILSLRLQHKTDR 120 +LEL L+ + E+VVSLGGG+L+NDRCF LI TGTLVY+ S+P +L+ RL HK+DR Sbjct: 61 DLELMVLQNYSGKSELVVSLGGGLLQNDRCFSLIISTGTLVYLHSNPLVLAKRLSHKSDR 120 Query: 121 PLLKGPNGEKLSREQVEQRISEILEKREPRYQKADLIIVTDSKKIGSTVEEMTRKIERHI 180 PL+KG +G++LSR+ +EQ+I +LE+REPRY+ A + + TD+K+IG+TVEE+TRKIER+I Sbjct: 121 PLMKGEDGQRLSRDAIEQKILNMLEQREPRYKTAQITVETDTKRIGTTVEELTRKIERYI 180 Query: 181 RRVER 185 RR E+ Sbjct: 181 RRCEK 185 Lambda K H 0.317 0.137 0.370 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: 188 Number of extensions: 3 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: 187 Length of database: 197 Length adjustment: 20 Effective length of query: 167 Effective length of database: 177 Effective search space: 29559 Effective search space used: 29559 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 (21.6 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