Align glucokinase; EC 2.7.1.2 (characterized)
to candidate WP_087505883.1 CBE68_RS09735 ROK family transcriptional regulator
Query= CharProtDB::CH_014478 (324 letters) >NCBI__GCF_002165625.1:WP_087505883.1 Length = 407 Score = 112 bits (281), Expect = 1e-29 Identities = 71/247 (28%), Positives = 126/247 (51%), Gaps = 8/247 (3%) Query: 65 KSRLVGIGIGAPGPVNFANGSIEVAVNLGWEK-FPIKDILEVETSLPVVVDNDANIAAIG 123 K +L+ I I PG +N G I + ++ E+ F I D + ++P + N A+ Sbjct: 144 KHQLIAIAITCPGLLNTETGVISYSPHIPLEQPFAIADEISAVFNVPCYLGNSTRSLALA 203 Query: 124 EMWKGAGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCNCGK 183 E + G +D++ V + G+G G+I +GE++ G GEIGHI P G C+CG Sbjct: 204 EHYFGNAKDCRDVVVVRIDHGIGAGIIMDGEVLMGQGLNRGEIGHIQVNPL-GERCHCGN 262 Query: 184 TGCLETIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAMHVV 243 GCLET+A+ +V+ +++L ++ + L +T + AA + D LA V+ Sbjct: 263 FGCLETVAADDAVVK-RVKQLKDSGYATGLSMT-----NLTMSAICQAALAGDQLAQQVL 316 Query: 244 DKVAFHLGLALANSANALNPEKIVLGGGVSRAGEVLLAPVRDYFKRFAFPRVAQGAELAI 303 + A +G ALA + N LNP+KI++GG + + +V+ + ++ Q ++ Sbjct: 317 KETAEAIGKALATTVNLLNPQKIIIGGDIVQGWDVVAPVLNASLQQQTLELFYQRLQVKA 376 Query: 304 ATLGNDA 310 +T+ D+ Sbjct: 377 STISQDS 383 Lambda K H 0.316 0.137 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: 251 Number of extensions: 11 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: 324 Length of database: 407 Length adjustment: 29 Effective length of query: 295 Effective length of database: 378 Effective search space: 111510 Effective search space used: 111510 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. 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