Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_017617089.1 CDO52_RS11555 ROK family glucokinase
Query= BRENDA::B1VZT1 (313 letters) >NCBI__GCF_002263495.1:WP_017617089.1 Length = 317 Score = 333 bits (853), Expect = 4e-96 Identities = 166/317 (52%), Positives = 221/317 (69%), Gaps = 5/317 (1%) Query: 1 MGLTIGVDIGGTKIAAGVVDEEGRILSTFKVATPPT--AEGIVDAICAAVAGASE---GH 55 M LTIGVDIGGTK+AAG+VD +GRIL PT +E + D I V E GH Sbjct: 1 MRLTIGVDIGGTKVAAGMVDPDGRILGDVVRYPTPTNDSEALADVIGRVVVELRERHTGH 60 Query: 56 DVEAVGIGAAGYVDDKRATVLFAPNIDWRHEPLKDKVEQRVGLPVVVENDANAAAWGEYR 115 D+ AVG+G AG+VD+ RA ++ A N+ +P+ +++ +R+ LPVVVENDANAAAW E R Sbjct: 61 DIAAVGVGIAGFVDEDRARIVLAANLGLSDDPITERIRRRIDLPVVVENDANAAAWAEAR 120 Query: 116 FGAGQGHDDVICITLGTGLGGGIIIGNKLRRGRFGVAAEFGHIRVVPDGLLCGCGSQGCW 175 FGAG+G D V+ +TLGTG+GGGI++ +L+RGR+GVAAE GH R+V G CGCG+ GCW Sbjct: 121 FGAGRGSDHVVLVTLGTGVGGGIVMDGRLQRGRYGVAAEVGHYRMVRHGRRCGCGNNGCW 180 Query: 176 EQYASGRALVRYAKQRANATPENAAVLLGLGDGSVDGIEGKHISEAARQGDPVAVDSFRE 235 EQYASGRALV A+ A P AA LL L +G + I G I++AA +GD A++ FR Sbjct: 181 EQYASGRALVAEAQDLATTDPVRAAYLLKLAEGDISRIRGPEITQAALEGDEGALECFRA 240 Query: 236 LARWAGAGLADLASLFDPSAFIVGGGVSDEGELVLDPIRKSFRRWLIGGEWRPHAQVLAA 295 + W G GLADLA++ DP F+VGGGVS+ G+++L+P R SF++ + G R A + A Sbjct: 241 VGEWVGLGLADLAAILDPECFVVGGGVSEAGDILLEPARASFKKHVTGRATRRLADIRTA 300 Query: 296 QLGGKAGLVGAADLARQ 312 +LG +AG+VGAADLAR+ Sbjct: 301 ELGPQAGIVGAADLARR 317 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: 387 Number of extensions: 19 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: 317 Length adjustment: 27 Effective length of query: 286 Effective length of database: 290 Effective search space: 82940 Effective search space used: 82940 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: 48 (23.1 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