Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_011840150.1 RSPH17029_RS00375 ROK family protein
Query= reanno::SB2B:6938110 (299 letters) >NCBI__GCF_000015985.1:WP_011840150.1 Length = 295 Score = 147 bits (371), Expect = 3e-40 Identities = 96/263 (36%), Positives = 137/263 (52%), Gaps = 10/263 (3%) Query: 2 MRMGVDLGGTKIELV-ALGEDGSELFRKRIATPREYQGTLNAVVTLVNEAEATLGTQGSL 60 M + D+GG++I A D E +R P + G + A+ L+ E EAT SL Sbjct: 1 MLIAFDIGGSRIRAARAFAPDDLEPLGER-PMPLSFPGFVAALRDLMPE-EAT-----SL 53 Query: 61 GIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAAA 120 I I GV+ P TG + AN +N L DL A L R V + NDA+CF ++EA+ G Sbjct: 54 AIAIAGVVDPDTGRITAANLPAVNQRALAADLCAALGRPVWIGNDADCFVLTEALLGVGR 113 Query: 121 GKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLPWMRP--DEFNTTECFCGNK 178 G R VFG ILG+G G G+ DGR+ G GI GEWGH P+ RP + C CG Sbjct: 114 GHRSVFGIILGSGVGGGIVLDGRLLTGAGGIAGEWGHAPVLDQRPLGRDLPHLPCGCGQS 173 Query: 179 DCIETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHVIN 238 C++T+ S G R G + EI++ AG+ A + +L+ +A LA ++N Sbjct: 174 GCVDTYGSARGIERLHLALCGQRLDSREILAAWRAGEMAAAETVEVWLELVAGPLAMLVN 233 Query: 239 MLDPDAIVLGGGMSNVQAIYARL 261 ++ P + +GGG+SN + A L Sbjct: 234 VIGPSVVPVGGGLSNDGDLVAAL 256 Lambda K H 0.320 0.139 0.429 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: 286 Number of extensions: 14 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: 299 Length of database: 295 Length adjustment: 26 Effective length of query: 273 Effective length of database: 269 Effective search space: 73437 Effective search space used: 73437 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. 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