Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_052668142.1 NITAL_RS20430 ROK family protein
Query= BRENDA::B1VZT1 (313 letters) >NCBI__GCF_000969705.1:WP_052668142.1 Length = 316 Score = 166 bits (419), Expect = 9e-46 Identities = 115/318 (36%), Positives = 168/318 (52%), Gaps = 17/318 (5%) Query: 4 TIGVDIGGTKIAAGVVDEEGRILSTFKVATPPTAE--GIVDAICAAVAGASEG-----HD 56 T+GVD+GGT I+ V+D E R++ ++ TP + G+ D + AAV A + D Sbjct: 3 TVGVDLGGTNISTVVLDGE-RVIGRSRLKTPTGGDRTGVTDVMAAAVHDALDDAGVTRDD 61 Query: 57 VEAVGIGAAGYVDDKRATVLFAPNIDWRHE--PLKDKVEQRVGLPVVVENDANAAAWGEY 114 ++ VG+G+ G V D TV A N+ E L D +E + +PV V ND AAA GE+ Sbjct: 62 LDVVGVGSPGVVID--GTVGGAANVPDFQERFSLADLLESDLRVPVRVSNDVTAAAVGEH 119 Query: 115 RFGAGQGHDDVICITLGTGLGGGIIIGNKLRRGRFGVAAEFGHIRVVPDGLLCGCGSQGC 174 R GAG+G D ++C+ +GTG+GGG+++G + GR G A EFGH V G +C CG +GC Sbjct: 120 RLGAGRGCDALLCVFVGTGVGGGLVLGGQPWEGR-GGAGEFGHTIVRQGGAVCPCGRRGC 178 Query: 175 WEQYASGRALVRYAKQRANATPENAAVLLGLGDGSVDGIEGKHISEAARQGDPVAVDSFR 234 E YA GR + A +RA A + + + +EA +GD + D Sbjct: 179 VEAYA-GRRAMALAAERARAAGRATVLFDVMAEKGKTTPSAGVFAEALARGDELVADLLD 237 Query: 235 ELARWAGAGLADLASLFDPSAFIVGGGVSDE-GELVLDPIRKSFRRWLIGGEWRPHAQVL 293 + GAG+A +L D ++GGGV D G+ + + R L P +V+ Sbjct: 238 DAVSALGAGIASAVNLLDIDLVVLGGGVGDRLGDDFRTRVEAAARPLLF--LQPPRVRVV 295 Query: 294 AAQLGGKAGLVGAADLAR 311 AA+LG G +GAA LAR Sbjct: 296 AAELGDDGGAIGAALLAR 313 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: 395 Number of extensions: 27 Number of successful extensions: 5 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: 316 Length adjustment: 27 Effective length of query: 286 Effective length of database: 289 Effective search space: 82654 Effective search space used: 82654 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