Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_012332266.1 M446_RS11440 helix-turn-helix domain-containing protein
Query= curated2:Q67N09 (174 letters) >NCBI__GCF_000019365.1:WP_012332266.1 Length = 328 Score = 101 bits (251), Expect = 1e-26 Identities = 61/154 (39%), Positives = 86/154 (55%), Gaps = 4/154 (2%) Query: 3 IVLVGLMGSGKTAVGRLLAERLGRPFVDTDRLVEADAGRTVADIFAAEGEEGFRRREAEV 62 + L+GL G+GK+ +GR+LAERLG FV+ +R +E + G +VA+IFA G+EG+RR E Sbjct: 151 VALIGLRGAGKSTLGRILAERLGWRFVELNREIERENGLSVAEIFAIYGQEGYRRLEQAA 210 Query: 63 VARAAAGDNQVI-ATGGGAVLRTENREALRRTGFVIWLDAEPETLYDRARGQ---GLHRR 118 + + A + V+ ATGG V + L F +WL A+PE R R Q G R Sbjct: 211 LRKFAVDEGPVVLATGGAIVAEPLTLDLLLSAFFTVWLKAQPEDHLRRVREQTALGAARP 270 Query: 119 PLLSGPDPLGRLRALAAARRPFYAQAAHVRICTD 152 L L L+A+ +R P YA+A V TD Sbjct: 271 RLPDNDSALRELKAVLLSREPLYARARAVIDTTD 304 Lambda K H 0.321 0.138 0.395 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: 130 Number of extensions: 5 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: 174 Length of database: 328 Length adjustment: 23 Effective length of query: 151 Effective length of database: 305 Effective search space: 46055 Effective search space used: 46055 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: 46 (22.3 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