Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_072909858.1 BUB13_RS16435 shikimate kinase
Query= curated2:B5YHI3 (173 letters) >NCBI__GCF_900142125.1:WP_072909858.1 Length = 166 Score = 127 bits (319), Expect = 1e-34 Identities = 73/162 (45%), Positives = 102/162 (62%), Gaps = 2/162 (1%) Query: 3 NIVLIGFMGTGKTSVGKLVAKKLGFDFVDVDEVIEKATGMEISEIFSKFGESRFRDIEEE 62 NIVLIG+ GTGK+ VG+L+ KK G V +DE I K GM I +I KFG RFR++E E Sbjct: 2 NIVLIGYRGTGKSHVGQLLGKKFGRKVVSMDEEIVKTAGMPIPQIVEKFGWDRFREMETE 61 Query: 63 MIKLITPKKRQVIATGGGVVLRDENMKRLKKDGVIFCLRASENVIFERLKQTTNRP-LLQ 121 + + + +I GGG++ R EN + L+++G +F LRAS I R+K T RP L++ Sbjct: 62 EARKLAGHDQLIIDCGGGIIERTENTEILQQNGNVFWLRASVESIVARIKDGTQRPALVE 121 Query: 122 VENPEERIKELLQKRMPLYE-KADFCIDTEGLTPEEVAEKII 162 + E + E+LQ+R PLY A IDT+ TPE+VA+ II Sbjct: 122 GKTFTEEVAEVLQRRTPLYRAAAHHEIDTDNRTPEQVAKAII 163 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: 106 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: 166 Length adjustment: 18 Effective length of query: 155 Effective length of database: 148 Effective search space: 22940 Effective search space used: 22940 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: 43 (21.2 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