Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_084057691.1 B9A12_RS09725 ROK family protein
Query= BRENDA::Q8RDE9 (315 letters) >NCBI__GCF_900176285.1:WP_084057691.1 Length = 325 Score = 185 bits (470), Expect = 1e-51 Identities = 95/314 (30%), Positives = 166/314 (52%), Gaps = 3/314 (0%) Query: 3 KFLCGVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGLEM 62 K + GVD+GGT + ++D G ++ K + +++GP+ + R+ + +L D GL Sbjct: 4 KCVIGVDIGGTHMRCALMDRKGTVLAFRKDRSRSDEGPEALTRRLVQQCRDLLADGGLSN 63 Query: 63 SNLKGIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAAIGE 122 + L +G+G G L+ G ++ PNLP + P+ + + L + V +ENDAN +GE Sbjct: 64 ARLGAVGLGVAGKLDTASGTILFSPNLPSLAGFPLAVRVQEALQVPVAMENDANVFGLGE 123 Query: 123 HLFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSN-AAEIGHHTINFDGPRCNCGNY 181 G R V N++ +T+ TG+GG G+L+ G+ + EIGH ++ GP C CG Sbjct: 124 AWLGKARNVSNWIGVTLGTGVGGCFFANGRLWQGDRLGFSGEIGHMIVDPQGPECACGQK 183 Query: 182 GCFEAYASGTAIARFAREGIEKGIKTK--IKELAGEGEVKAEHVFEAAKLGDEFAKELVE 239 GC EA+AS TA+ + R+ ++ + ++E ++ A ++ AA+ GD A+ L Sbjct: 184 GCLEAHASATALVQGVRQAQKEAVPLSDLLQEALRRDQLTAHTIYRAARGGDPVARRLFA 243 Query: 240 KEAFYLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKMMETVRKKALKPNAEVCEVVKA 299 + + L V ++N+ F IGGGVSA WD M++ ++ + + V + Sbjct: 244 RMGWALAVALSNLFTFLGISTAVIGGGVSASWDQFAPAMLDYFQQVPSMLDPQSIHVHRT 303 Query: 300 QLGENIGVLGAAAL 313 +L + + GAA+L Sbjct: 304 ELEDRASIYGAASL 317 Lambda K H 0.316 0.138 0.398 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: 246 Number of extensions: 14 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: 315 Length of database: 325 Length adjustment: 28 Effective length of query: 287 Effective length of database: 297 Effective search space: 85239 Effective search space used: 85239 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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