Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate 352021 BT2493 ROK family transcriptional repressor, with glucokinase domain (NCBI ptt file)
Query= BRENDA::Q8R8N4 (312 letters) >FitnessBrowser__Btheta:352021 Length = 326 Score = 191 bits (484), Expect = 3e-53 Identities = 116/314 (36%), Positives = 178/314 (56%), Gaps = 10/314 (3%) Query: 3 IGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGIS--VK 60 +G+D+GGTN G+V+ G IIA+ S T GY A E+ LL + + V Sbjct: 11 VGIDIGGTNTVFGIVDARGTIIASSSIKTA---GYPTAAEYADEVCKNLLPLIIANGGVD 67 Query: 61 DVKSMGIGVPGVADNEKGIVIRAVNLFWTKV-PLAKEIRKYIDLPIYMENDANVAALAEA 119 ++ +G+G P + G + A NL W + PLA + + +P + NDAN AA+ E Sbjct: 68 KIRGIGVGAPN-GNYYTGTIEFAPNLPWKGILPLAAMFEERLGIPTALTNDANAAAIGEM 126 Query: 120 TFGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGC 179 T+GA RG K + ITLGTGVGSG +++G++ G FA E+GH++ +G C CG+ GC Sbjct: 127 TYGAARGMKDFIMITLGTGVGSGIVINGQMVYGHDGFAGELGHVIARRDGRVCGCGRKGC 186 Query: 180 FETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFEEY 239 ETY SAT + R ++ + +L+ N E IT+K+V DAA Q D+ A +IFE Sbjct: 187 LETYCSATGVARTAREFLAARTDASLLR--NIPAENITSKDVYDAAVQGDKLAQEIFEFT 244 Query: 240 VKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRKAEL 299 L + + I PE I+L GG+A +GD+++KP++K + +NIL + +EL Sbjct: 245 GNILGEALADAIAFSSPEAIVLFGGLAKSGDYIMKPIQKAIDDNILNIYKGKTKLLVSEL 304 Query: 300 -GNDAGIIGAAILS 312 +DA ++GA+ L+ Sbjct: 305 KDSDAAVLGASALA 318 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: 334 Number of extensions: 13 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: 312 Length of database: 326 Length adjustment: 28 Effective length of query: 284 Effective length of database: 298 Effective search space: 84632 Effective search space used: 84632 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