Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate Ga0059261_4061 Ga0059261_4061 Transcriptional regulator/sugar kinase
Query= BRENDA::Q8R8N4 (312 letters) >FitnessBrowser__Korea:Ga0059261_4061 Length = 291 Score = 84.0 bits (206), Expect = 4e-21 Identities = 80/315 (25%), Positives = 132/315 (41%), Gaps = 44/315 (13%) Query: 3 IGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVKDV 62 + ++ GGT + LV ++G + T PE A + A L+F R ++ + Sbjct: 8 LAIETGGTKLLARLVRDEGVVAEARWPTTSPE------AAEAALLAFA--GRTPLAGVGI 59 Query: 63 KSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDANVAALAEATFG 122 + G V A G V+ WT L + + + +P+ ++ D N AALAEA G Sbjct: 60 AAFGPVVVDPAAANYGEVLATPKPGWTGANLRAALEQALGVPVAIDTDVNAAALAEAAAG 119 Query: 123 AGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGCFET 182 AG+G S +T+GTG+G+G DG+ +GA H PE+GH+ + Sbjct: 120 AGQGCSSLAYVTVGTGIGAGLARDGRTLTGALH--PEMGHVPV----------------- 160 Query: 183 YASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVID--AAKQYDEEALKIFEEYV 240 L EG +P F +G EG+ A + + E++ F Sbjct: 161 ------LRFEG------DPTPSACPFHSGCAEGMAAGPAVQRRLGGKLLEDSPADFAAVA 208 Query: 241 KYLAVGIVNIINLFDPEVIILGGGVANA---GDFLLKPLKKEVAENILFKELPYADIRKA 297 YL I+ + P I++GGGV + G ++ + + + AD ++ Sbjct: 209 DYLGQLFATIVLAWSPHRIVVGGGVMDVPGLGKAATVRMRVALGGYGVGSAVGEADFIRS 268 Query: 298 ELGNDAGIIGAAILS 312 AG+ GA IL+ Sbjct: 269 AALEHAGLEGALILA 283 Lambda K H 0.318 0.140 0.397 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: 251 Number of extensions: 20 Number of successful extensions: 4 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: 312 Length of database: 291 Length adjustment: 27 Effective length of query: 285 Effective length of database: 264 Effective search space: 75240 Effective search space used: 75240 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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