Align glucokinase (EC 2.7.1.2) (characterized)
to candidate 354180 BT4654 ROK family transcriptional repressor, with glucokinase domain (NCBI ptt file)
Query= BRENDA::Q8RDE9 (315 letters) >FitnessBrowser__Btheta:354180 Length = 317 Score = 200 bits (508), Expect = 4e-56 Identities = 108/316 (34%), Positives = 177/316 (56%), Gaps = 8/316 (2%) Query: 2 KKFLCGVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGLE 61 K++ G+DLGGT + ++D NG K+P+ A+ + VI ++ +++ +V + Sbjct: 3 KEYAIGIDLGGTSVKYALIDNNGVFHFQGKLPSNADVSAEAVIGQLVKAVNEVKTFAEAK 62 Query: 62 MSNLKGIGIGSPGPLNAKKGIVIS-PPNLPHWSNVPIVEILSKRLGIEVRLENDANAAAI 120 + GIGIG+PG ++ IV+ N+ W N+ + + + K G+ +L NDAN + Sbjct: 63 RYTIAGIGIGTPGIVDCTNRIVLGGAENIQGWENLKLADRMEKETGLPTQLGNDANLMGL 122 Query: 121 GEHLFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINFDGPRCNCGN 180 GE ++G+G G + V++TV TGIGG VII+GKL++G + E+GH + +G C CG+ Sbjct: 123 GETMYGAGNGATHVVFLTVGTGIGGAVIIDGKLFNGYANRGTELGHVPLIANGEPCACGS 182 Query: 181 YGCFEAYASGTA-IARFAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKLGDEFAKELVE 239 GC E YAS A + RF++ E GI +E+ G E + K GD+ A E + Sbjct: 183 IGCLEHYASTAALVRRFSKRIAEAGISYPNEEING------ELIVRLYKQGDKIAAESLN 236 Query: 240 KEAFYLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKMMETVRKKALKPNAEVCEVVKA 299 + +LG GIA + ++P+++ IGGG+S D +K+ E + A+ A E++ A Sbjct: 237 EHCDFLGHGIAGFINIFSPQRVVIGGGLSEAGDFYIQKVSEKALRYAIPDCAVNTEIMAA 296 Query: 300 QLGENIGVLGAAALLL 315 LG G +GAA+L L Sbjct: 297 SLGNKAGSIGAASLFL 312 Lambda K H 0.316 0.138 0.398 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: 290 Number of extensions: 18 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: 315 Length of database: 317 Length adjustment: 27 Effective length of query: 288 Effective length of database: 290 Effective search space: 83520 Effective search space used: 83520 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 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