Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_008508951.1 BIBO1_RS14955 ROK family transcriptional regulator
Query= BRENDA::P54495 (321 letters) >NCBI__GCF_000182725.1:WP_008508951.1 Length = 374 Score = 122 bits (307), Expect = 1e-32 Identities = 81/245 (33%), Positives = 111/245 (45%), Gaps = 22/245 (8%) Query: 67 IGMGAPGPVDMAAGVVYETVNLGWKNYALKNHLETETGIPAVIENDANIAALGEMWKGAG 126 IGMG PGPVD A ++N GW++ A + +E E IP V+E++ AL E G G Sbjct: 141 IGMGVPGPVDQARRRNLLSINTGWRDVAFADAMEAELNIPTVVEHNVTAMALAEAHYGLG 200 Query: 127 DGAKDVILVTLGTGVGGGIIANGEIVHGINGAGGEIGHICSIPEGGAPCNCGKTGCIETI 186 G V+ V LGTG+G G++ +G E+GHI P+ GA C CG GC+ET Sbjct: 201 QGCPAVLYVYLGTGLGAGLVVDGMPFRPGGHGAVELGHIQIDPQ-GALCACGNRGCLETF 259 Query: 187 ASATGIVRIAKEKIANAKKTTRLKATEQLSARDVFEAAGENDEIALEVVDYVAKHLGLVL 246 S R+ +E+ A SA + A N + D VA H L Sbjct: 260 VSE----RVLRERGAG-------------SAEPLLAALARNPALH----DEVAGHFTTAL 298 Query: 247 GNLASSLNPSKIVLGGGVSRAGELLRSKVEKTFRKCAFPRAAQAADISIAALGNDAGVIG 306 N + L P IVLGG + A E +++ P I GN+AG +G Sbjct: 299 ANAVNLLTPDLIVLGGHFAEAPEAFYARLRCDLPPRVLPHMRDVLRIERGGFGNNAGAVG 358 Query: 307 GAWIA 311 A +A Sbjct: 359 AAAVA 363 Lambda K H 0.316 0.135 0.403 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: 266 Number of extensions: 15 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: 321 Length of database: 374 Length adjustment: 29 Effective length of query: 292 Effective length of database: 345 Effective search space: 100740 Effective search space used: 100740 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