Align glucokinase; EC 2.7.1.2 (characterized)
to candidate WP_003466468.1 J416_RS05305 ROK family glucokinase
Query= CharProtDB::CH_014478 (324 letters) >NCBI__GCF_000359605.1:WP_003466468.1 Length = 322 Score = 291 bits (745), Expect = 1e-83 Identities = 144/317 (45%), Positives = 208/317 (65%), Gaps = 2/317 (0%) Query: 3 MDDKWLVGVDLGGTTIKMAFINHYGEIIHKWEINTDVSEQGRKIPTDIAKAIDKKLNDLG 62 M DK +GVD+GGTT+K A I GE+I WEI T + +G ++P DI +I +L Sbjct: 1 MRDKVTIGVDIGGTTVKHAIIREDGEMITNWEIPTRLDHKGAQVPHDIWSSIQDQLVQQN 60 Query: 63 EVKSRLVGIGIGAPGPVNFANGSIEVAVNLGWEKFPIKDILEVETSLPVVVDNDANIAAI 122 K ++GIG+GAPG ++ G + +AVN+GWE + +K IL+ + + V V+NDAN+AA+ Sbjct: 61 IDKRDIIGIGVGAPGFIDPETGIVTIAVNIGWENYDLKQILQDLSGVSVFVENDANVAAL 120 Query: 123 GEMWKGAGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCNCG 182 GE WKGAG+ +++ VTLGTGVGGG+I+N I+ G NG GEIGHIT + + GA CNCG Sbjct: 121 GENWKGAGNQVHNMIAVTLGTGVGGGIISNHTIINGANGTGGEIGHIT-VEKDGASCNCG 179 Query: 183 KTGCLETIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAMHV 242 + GCLET+ASATGIVR +E+ ++ +++ + +T+KD+F+ A++ D + Sbjct: 180 RKGCLETVASATGIVR-QAKEMIDSGVKTDIVNQVNDEASITTKDIFEVAKTGDQAMNEL 238 Query: 243 VDKVAFHLGLALANSANALNPEKIVLGGGVSRAGEVLLAPVRDYFKRFAFPRVAQGAELA 302 +D V LG ALA A NP KIV+GGGVS+AG+ LL P++ F+ + PR E Sbjct: 239 LDHVIDVLGFALAGVAMTTNPAKIVIGGGVSKAGDQLLQPLKKKFESYCLPRTTHACEFV 298 Query: 303 IATLGNDAGIIGGAWLV 319 +A L NDAG+ G A++V Sbjct: 299 LAQLENDAGVYGAAYMV 315 Lambda K H 0.316 0.137 0.404 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: 333 Number of extensions: 16 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: 324 Length of database: 322 Length adjustment: 28 Effective length of query: 296 Effective length of database: 294 Effective search space: 87024 Effective search space used: 87024 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: 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