Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate BPHYT_RS13350 BPHYT_RS13350 shikimate kinase
Query= curated2:Q2JRJ6 (189 letters) >FitnessBrowser__BFirm:BPHYT_RS13350 Length = 324 Score = 90.5 bits (223), Expect = 3e-23 Identities = 59/174 (33%), Positives = 94/174 (54%), Gaps = 3/174 (1%) Query: 15 VYLIGMMASGKSTLGAELAAQLRRPFFDTDALVEQVAGCSIAQIFAEQGEAHFRELETQV 74 + LIG+ +GKSTLG LA + + PF + ++EQ+AGC ++I + G A +R E + Sbjct: 146 IALIGLRGAGKSTLGRMLAQERKVPFVELTRVIEQLAGCPPSEIHSLYGAAAYRRYEHRA 205 Query: 75 L-AQLSGYTRLVVATGGGIVLRPKNW-SYLHHGLTVWLDAAPELIWQRLKRDPGQRPLLQ 132 L A + + R V+A+ GG+V + + L H TVWL AAPE +R+ RP+ Sbjct: 206 LEAVIQEHERAVIASPGGLVSESGTFNTLLSHCYTVWLQAAPEEHMRRVVAQGDLRPMSG 265 Query: 133 TPDPQAALQRLMQEREPFYAQADVRVPIHSEASPSQLAEQVWQAICARLRAQPP 186 + L+R++ R YA+AD+ SE + + Q+ + ARL A+ P Sbjct: 266 NKEAMDDLKRILAGRSELYARADMTFDT-SEKTLADAYLQLRDRLAARLAAESP 318 Lambda K H 0.321 0.134 0.408 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: 186 Number of extensions: 11 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: 189 Length of database: 324 Length adjustment: 24 Effective length of query: 165 Effective length of database: 300 Effective search space: 49500 Effective search space used: 49500 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 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 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