Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_041098435.1 SUTH_RS08165 helix-turn-helix transcriptional regulator
Query= curated2:Q5NPY7 (176 letters) >NCBI__GCF_000828635.1:WP_041098435.1 Length = 298 Score = 100 bits (248), Expect = 3e-26 Identities = 61/157 (38%), Positives = 86/157 (54%), Gaps = 3/157 (1%) Query: 11 RTITLIGMMGVGKSTIGRRLASQLNMPFSDSDLEIEEAAGQSITEIFARYGENYFRNGER 70 + I L+G+ G GKST+GR LAS+L++PF + + IE AG S+ EIF YG+ FR ER Sbjct: 131 KRIALVGLRGAGKSTLGRALASELSLPFVELNSAIEAEAGMSLNEIFMLYGQPGFRRLER 190 Query: 71 RVISRLIA-GEPKVLAVGGGAFMDEETRKLVLEKTLAIWVKADIDTLAERVTKQAD-RPL 128 R + IA E V+ VGGG + ET L+L +WVKA + RV Q D RP+ Sbjct: 191 RCLENFIAQHESAVITVGGGIVSEAETFNLLLMNCYTVWVKATPEEHMSRVVAQGDLRPM 250 Query: 129 LIGHDVRTRLQELADIRDSFYAMAPLHV-WTGAQPHE 164 + ++ + R+ Y+ A + TG QP E Sbjct: 251 EGNTEAMEDMRRILVAREPLYSKADFTLDTTGRQPEE 287 Lambda K H 0.320 0.136 0.390 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: 113 Number of extensions: 7 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: 176 Length of database: 298 Length adjustment: 23 Effective length of query: 153 Effective length of database: 275 Effective search space: 42075 Effective search space used: 42075 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: 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