Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_011604741.1 FRAAL_RS15740 serine transporter
Query= curated2:Q47JK7 (183 letters) >NCBI__GCF_000058485.1:WP_011604741.1 Length = 188 Score = 94.0 bits (232), Expect = 1e-24 Identities = 55/145 (37%), Positives = 81/145 (55%), Gaps = 3/145 (2%) Query: 18 IYLVGLMGAGKTTVGRQLARRLSRPFFDTDHEIVERTGVPIPTIFEIEGEEGFRRREAQT 77 I+LVGLMG+GK+TVGR LA RL RP+ D D + +RTG+ P + ++ G +E++ Sbjct: 25 IFLVGLMGSGKSTVGRALAARLGRPYLDNDALLQQRTGLDAPALADL-GRAALHDQESRQ 83 Query: 78 IYD-LTAENNIVLATGGGVVINPENRRRLHDTGWVVYLNVSPVLLYERTRHDRNRPLLRV 136 ++ L V + NP++ R+ D G VVYL +P L R + RP L Sbjct: 84 LHALLDTPAPYVAGVAASIADNPDDLGRIVDAGRVVYLRATPRTLARRVGRGQGRPWLD- 142 Query: 137 EDPLAKLEELHSIRDPLYREVAHIV 161 D L+ L E+ + RD +YR V H+V Sbjct: 143 GDLLSTLNEMFAARDDVYRRVGHVV 167 Lambda K H 0.321 0.140 0.404 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: 110 Number of extensions: 6 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: 183 Length of database: 188 Length adjustment: 19 Effective length of query: 164 Effective length of database: 169 Effective search space: 27716 Effective search space used: 27716 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 (21.9 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