Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate RR42_RS07515 RR42_RS07515 transcriptional regulator
Query= curated2:Q89XW7 (207 letters) >FitnessBrowser__Cup4G11:RR42_RS07515 Length = 312 Score = 94.0 bits (232), Expect = 3e-24 Identities = 58/170 (34%), Positives = 93/170 (54%), Gaps = 6/170 (3%) Query: 23 RSIVLVGMMGVGKSTIGRRMAARLKLPFVDADTEIEAAAGMTIPEIFERHGEGHFRDGEA 82 R I L+G+ G GKST+GR +AA +++PFV+ + IE AG ++ EI +G+ +R E Sbjct: 142 RRITLIGLRGAGKSTLGRALAAAMEVPFVELNGVIEQEAGASLAEIHSLYGQAAYRRYEM 201 Query: 83 RVIARLL-DGGPVVLATGGGAFMREETRARIAAKAVSIWLKADHDVIMRRVRRRAD-RPL 140 R + R+L + +VLAT G T + A+ ++W+K + M RV + D RP+ Sbjct: 202 RALERVLRENDRMVLATPGSLVSEPSTFNLLLARCYTVWVKTTPEEHMARVVAQGDMRPM 261 Query: 141 LQTADPEGTVTRLLTEREPVYSHADLTIASRDVPHDKIVEECIETLRAHL 190 + + R+L R P+YS AD+TI + + ++ LRAHL Sbjct: 262 EGNREAMDDLRRILLARTPLYSRADVTIDT----SGQDPTTSLQALRAHL 307 Lambda K H 0.320 0.135 0.386 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: 151 Number of extensions: 10 Number of successful extensions: 3 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: 207 Length of database: 312 Length adjustment: 24 Effective length of query: 183 Effective length of database: 288 Effective search space: 52704 Effective search space used: 52704 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: 47 (22.7 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