Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_011612407.1 TERY_RS13830 ROK family protein
Query= BRENDA::Q8RDE9 (315 letters) >NCBI__GCF_000014265.1:WP_011612407.1 Length = 303 Score = 183 bits (465), Expect = 4e-51 Identities = 103/315 (32%), Positives = 166/315 (52%), Gaps = 22/315 (6%) Query: 1 MKKFLCGVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGL 60 M + G+D+GGT I G +G +S+ +PT P VI+ I+E I ++K+ + Sbjct: 1 MNSLVIGIDIGGTSIKLGCFGRDGVCHQSLTVPTPRPATPKAVIDLIKEVISMMIKEPQI 60 Query: 61 -EMSNLKGIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAA 119 + ++GIGIG PGP++A+ I NL W +VP+ ++L ++ G+ V + NDAN A Sbjct: 61 YNLGPIQGIGIGVPGPVDAEGKTSIIAINLTDWQDVPLAKLLEEKTGLPVVIANDANCAG 120 Query: 120 IGEHLFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINFDGPRCNCG 179 +GE G+G N + +T+ TG+GG +I+ +L+ G A E+G T+N DGP+CN G Sbjct: 121 LGEAWLGAGSQYKNLIMLTLGTGVGGAIILNSQLFVGHQGAAGELGLITLNLDGPKCNSG 180 Query: 180 NYGCFEAYASGTAIAR-FAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKLGDEFAKELV 238 N G E Y S A+ R +E +E + A GD+FA E Sbjct: 181 NNGSLEQYISVQAVRRETGKEPLE--------------------LANLALAGDKFALEFW 220 Query: 239 EKEAFYLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKMMETVRKKALKPNAEVCEVVK 298 + LG G+A+++ P + IGGG+SA + V+++ L ++ +++ Sbjct: 221 QNYGRLLGAGLASLIYILTPEAVIIGGGISAAAKLFLPATKAEVKRRVLLTSSLKLQLLI 280 Query: 299 AQLGENIGVLGAAAL 313 A+LG GV+GAA L Sbjct: 281 AKLGNQAGVIGAAKL 295 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: 257 Number of extensions: 14 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: 303 Length adjustment: 27 Effective length of query: 288 Effective length of database: 276 Effective search space: 79488 Effective search space used: 79488 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