Align glucokinase; EC 2.7.1.2 (characterized)
to candidate WP_038019118.1 HA49_RS15320 ROK family protein
Query= CharProtDB::CH_014478 (324 letters) >NCBI__GCF_000757425.2:WP_038019118.1 Length = 406 Score = 123 bits (309), Expect = 7e-33 Identities = 87/275 (31%), Positives = 131/275 (47%), Gaps = 9/275 (3%) Query: 9 VGVDLGGTTIKMAFINHYGEIIHKWEINTDVSEQGRKIPTDIAKAIDKKLNDLGEVKSRL 68 + V LG +A + G+++ + D ++Q + + + AI+ + + L Sbjct: 89 IAVRLGRQDATLALFDLGGQLLTEQHYPIDQTDQ-QAVEQALFSAIEAFIAQQRPLLDEL 147 Query: 69 VGIGIGAPGPVNFANGSIEVAVNLGWEKFPIKDILEVETSLPVVVDNDANIAAIGEMWKG 128 + I + PG V+ G + ++G +P+ D L + V +D A+ E + G Sbjct: 148 IAISVILPGLVDPVQGIVRFMPHIGKTHWPLVDNLTARFNTASFVGHDIRSLALAEHYFG 207 Query: 129 AGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCNCGKTGCLE 188 A D L V + G G G+I NG I G NG GEIGHI P G C CG GCLE Sbjct: 208 ATRDCADSLLVRIHRGTGAGIIVNGNIFLGTNGNVGEIGHIQVDPL-GERCYCGNFGCLE 266 Query: 189 TIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAMHVVDKVAF 248 TIAS I++ + L P +L +T D+ AA D LA ++ +V Sbjct: 267 TIASNNAILQ-KAKTLVAQGYPGKL-----NESTMTISDICQAANQGDPLAQGLIKEVGT 320 Query: 249 HLGLALANSANALNPEKIVLGGGVSRAGEVLLAPV 283 HLG ALA + N NP+K+VL G ++ A E +L PV Sbjct: 321 HLGKALAIAINMFNPQKVVLAGELTEA-EAILFPV 354 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: 271 Number of extensions: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 324 Length of database: 406 Length adjustment: 29 Effective length of query: 295 Effective length of database: 377 Effective search space: 111215 Effective search space used: 111215 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: 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