Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_011189740.1 DP_RS12650 shikimate kinase
Query= curated2:B5YHI3 (173 letters) >NCBI__GCF_000025945.1:WP_011189740.1 Length = 177 Score = 99.8 bits (247), Expect = 2e-26 Identities = 57/166 (34%), Positives = 93/166 (56%), Gaps = 4/166 (2%) Query: 3 NIVLIGFMGTGKTSVGKLVAKKLGFDFVDVDEVIEKATGMEISEIFSKFGESRFRDIEEE 62 NI+LIG G+GK++VG ++AK LG +FVD D +I+ A + I G R+IEE Sbjct: 7 NIILIGMPGSGKSTVGVILAKTLGMEFVDTDILIQSAENRTLQTIVDNEGHIVLREIEER 66 Query: 63 MIKLITPKKRQVIATGGGVVLRDENMKRLKKDGVIFCLRASENVIFERLKQTTNRPLLQV 122 ++ L K+ ++ATGG + M LK+DG+I L A + R+ R + Sbjct: 67 VL-LTVDHKKHIVATGGSAAYSEAAMLHLKEDGIIVFLHADLAALCARIHNYETRGI--A 123 Query: 123 ENPEERIKELLQKRMPLYEK-ADFCIDTEGLTPEEVAEKIIKEYER 167 + PE+ +L +R+ LY+K AD I + ++ ++V E +I+E E+ Sbjct: 124 KRPEQSFDDLFAERLALYKKYADITILSSEISQDDVVETVIREVEK 169 Lambda K H 0.318 0.138 0.376 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: 99 Number of extensions: 5 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: 173 Length of database: 177 Length adjustment: 19 Effective length of query: 154 Effective length of database: 158 Effective search space: 24332 Effective search space used: 24332 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