Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_012589212.1 MSIL_RS00835 glucokinase
Query= curated2:B9JYQ5 (340 letters) >NCBI__GCF_000021745.1:WP_012589212.1 Length = 343 Score = 213 bits (543), Expect = 4e-60 Identities = 131/332 (39%), Positives = 172/332 (51%), Gaps = 6/332 (1%) Query: 11 PFPVLVGDIGGTNARFWILMDAHAAPKEFANIHTADFPTIDQAIQDCILDKSGF--QPRS 68 PFP+++ DIGGTNARF + A I TAD+ + A+ + GF +PRS Sbjct: 15 PFPIMLCDIGGTNARFALKSAPGAPLLPGPPIKTADYSCFEAALSTAFV---GFAVKPRS 71 Query: 69 AILAVAGPIKDDEIPLTNCPWVIRPKAMIADLGFDDVLVVNDFEAQALAAASLGRNDREP 128 I AGPI LTN W I A+ +L D L++NDFEAQAL L + Sbjct: 72 VIACAAGPISGRSAKLTNAAWEIDGAAIARELSLDQGLLLNDFEAQALTLPVLEHDWTTH 131 Query: 129 IGPLTETSLNSRVILGPGTGLGVGGLLYTHHTWFPVPGEGGHVDIGPRSDRDWQIFPHIE 188 IGP E + R+++G GTGLG L+ + + E GHVD P + I+PHI Sbjct: 132 IGPPVEAAPGVRLVIGVGTGLGAAALVEVEGRYLALASEAGHVDFAPVGAVEAAIWPHIR 191 Query: 189 RIE-GRISGEQILCGRGILHLYNAICAADGIEPVWTDPADVTQHALKGNDPVCVETMTLF 247 + GRIS E IL G GI L+ A CAA G+ P D V + AL D T+ LF Sbjct: 192 MSDQGRISAETILSGHGIARLHQARCAAAGLPPPTLDEIGVVREALAAPDGEEARTLGLF 251 Query: 248 VTYLGRIAGDMALVFMARGGVFLSGGISQKIIPLLKSPVFRAAFEDKAPHTEMMKTIPTF 307 + R AGD+ L +A+GGV SGG+ ++ L FRA FEDKAP EMM+ I T Sbjct: 252 WVLVARCAGDLTLNLLAKGGVIFSGGVLPRLTAFLDPAQFRARFEDKAPFGEMMQQIGTR 311 Query: 308 VAIHPQAALSGLAAYARTPSSYGVKHEGRRWQ 339 + I + L GLAA A P Y + + R W+ Sbjct: 312 LVIANEVVLPGLAAIAVDPDRYIIDYAARAWR 343 Lambda K H 0.322 0.140 0.445 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: 311 Number of extensions: 11 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: 340 Length of database: 343 Length adjustment: 29 Effective length of query: 311 Effective length of database: 314 Effective search space: 97654 Effective search space used: 97654 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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