Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_017620227.1 CDO52_RS05395 ROK family glucokinase
Query= BRENDA::B1VZT1 (313 letters) >NCBI__GCF_002263495.1:WP_017620227.1 Length = 344 Score = 323 bits (828), Expect = 4e-93 Identities = 159/313 (50%), Positives = 220/313 (70%), Gaps = 3/313 (0%) Query: 2 GLTIGVDIGGTKIAAGVVDEEGRILSTFKVATPPTAEG---IVDAICAAVAGASEGHDVE 58 GLT+G+DIGG+K+AAGVV+ GR+L+ + TP ++ + D I + + + V Sbjct: 13 GLTVGIDIGGSKVAAGVVNPSGRVLARRRTETPDKSKSPKVVEDTIVSVIEELRREYPVH 72 Query: 59 AVGIGAAGYVDDKRATVLFAPNIDWRHEPLKDKVEQRVGLPVVVENDANAAAWGEYRFGA 118 AVG+GAAG+VD++RA+VLFAP++ WR EPL++ + QR+ LPVVVENDANA+AW E R GA Sbjct: 73 AVGVGAAGFVDEQRASVLFAPHLAWRKEPLREALTQRLELPVVVENDANASAWAEVRVGA 132 Query: 119 GQGHDDVICITLGTGLGGGIIIGNKLRRGRFGVAAEFGHIRVVPDGLLCGCGSQGCWEQY 178 G+G DD++ + LGTG+GG II+ KL RGR+G+A EFGH+ VVP G C CG++GCWEQY Sbjct: 133 GRGVDDILVVNLGTGIGGAIILDGKLHRGRYGIAGEFGHMTVVPGGHRCECGNRGCWEQY 192 Query: 179 ASGRALVRYAKQRANATPENAAVLLGLGDGSVDGIEGKHISEAARQGDPVAVDSFRELAR 238 ASG A+ R A++ A A A L+ G I G +S+ AR+GD +V+ + Sbjct: 193 ASGNAVTRDARELAAADSPVARGLIQAVGGDPALITGPLVSDLAREGDRASVELLEDAGG 252 Query: 239 WAGAGLADLASLFDPSAFIVGGGVSDEGELVLDPIRKSFRRWLIGGEWRPHAQVLAAQLG 298 W G GLA+LA+ FDP FI+GGGVSD G+L+L P R +FRR L G +RP A+++ A+LG Sbjct: 253 WLGIGLANLAAAFDPELFIIGGGVSDCGDLLLGPARTAFRRQLTGRGYRPEARIVRAELG 312 Query: 299 GKAGLVGAADLAR 311 +AGL+GA+ LAR Sbjct: 313 NEAGLIGASLLAR 325 Lambda K H 0.319 0.140 0.427 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: 392 Number of extensions: 16 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: 313 Length of database: 344 Length adjustment: 28 Effective length of query: 285 Effective length of database: 316 Effective search space: 90060 Effective search space used: 90060 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 (21.7 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