Align Shikimate kinase; Short=SK; EC 2.7.1.71 (characterized, see rationale)
to candidate WP_017140213.1 RSPH17029_RS07480 shikimate kinase
Query= uniprot:A0A135IJ25 (196 letters) >NCBI__GCF_000015985.1:WP_017140213.1 Length = 199 Score = 229 bits (585), Expect = 2e-65 Identities = 121/181 (66%), Positives = 141/181 (77%), Gaps = 1/181 (0%) Query: 14 RRVPGALKKTIVMVGMMGAGKTAVGRALAARLQAPFLDSDHEIEAAANRTIPEIFARDGE 73 R+V LKKT+VMVGMMGAGKTAVG ALA L PFLDSD EIE AANRTI EIFARDGE Sbjct: 17 RQVMARLKKTVVMVGMMGAGKTAVGSALARGLNVPFLDSDEEIERAANRTIAEIFARDGE 76 Query: 74 PFFRKKERQVIRRLLDEERGVLSTGGGAFLAEENRQIISERGVAIWLNADLEVLWNRVKH 133 PFFR+KE QV+ RLL VLSTGGGAF+AE NR++I E+GV++WL ADL+VLW+RV+H Sbjct: 77 PFFREKESQVLARLLRGSPCVLSTGGGAFMAEGNRRMIREQGVSVWLKADLDVLWHRVRH 136 Query: 134 RDTRPLLRTEDPHATLSALYHDRVPYYAQADLTVVSDGQASIDEMVNRVVEALRARPDVL 193 + TRPLLRT +P TL AL R P YAQADL V S G+ ++++M RV EAL RPDVL Sbjct: 137 KATRPLLRTPNPRETLRALLEARDPVYAQADLAVES-GEGTVEQMAVRVREALATRPDVL 195 Query: 194 E 194 E Sbjct: 196 E 196 Lambda K H 0.319 0.135 0.387 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: 167 Number of extensions: 4 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: 196 Length of database: 199 Length adjustment: 20 Effective length of query: 176 Effective length of database: 179 Effective search space: 31504 Effective search space used: 31504 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 16 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