Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_041666889.1 SULKU_RS03215 shikimate kinase
Query= curated2:Q7VIH7 (167 letters) >NCBI__GCF_000183725.1:WP_041666889.1 Length = 159 Score = 109 bits (273), Expect = 2e-29 Identities = 62/156 (39%), Positives = 91/156 (58%), Gaps = 6/156 (3%) Query: 10 MGSGKTTIGREIALLGGRFLLDTDQIIEQNMGKSINEIFESVGESGFRRIESQLILWLSA 69 MG GK ++ REI L LDTD IIE ++I +IF GE FR +E ++ LWL Sbjct: 1 MGVGKGSVAREIVKLSDLVALDTDDIIESMENRTIKKIFAQEGEEYFRALERKVALWLQK 60 Query: 70 NVKNAVIATGGGMPIYNDVAYLGYVFWLDMSFESILKRLTI-----TEQEKRPLFSDISK 124 VK +I+TGGG +++ +G V +L FE+I R+ + KRPLF DI K Sbjct: 61 EVKGTLISTGGGFFKVPNLSKIGTVVYLSAPFETIYNRILAHPNAEKKLRKRPLFQDIEK 120 Query: 125 ARQLYNERKSIYKKQSKYIIN-GDASALEIARKIIE 159 AR+LY+ER +YKK + +I+ D E+A++I++ Sbjct: 121 ARKLYDERSVLYKKAADIVIDVSDKDIPEVAKEILK 156 Lambda K H 0.319 0.137 0.383 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: 79 Number of extensions: 4 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: 167 Length of database: 159 Length adjustment: 18 Effective length of query: 149 Effective length of database: 141 Effective search space: 21009 Effective search space used: 21009 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 (21.7 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