Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_009493232.1 MICLODRAFT_RS27800 glucokinase
Query= curated2:B9JYQ5 (340 letters) >NCBI__GCF_000262405.1:WP_009493232.1 Length = 332 Score = 230 bits (586), Expect = 4e-65 Identities = 134/330 (40%), Positives = 189/330 (57%), Gaps = 5/330 (1%) Query: 12 FPVLVGDIGGTNARFWILMDAHAAPKEFANIHTADFPTIDQAIQDCILDKSGFQPRSAIL 71 FPVL+GDIGGTNARF +L AA K TA P AI+ + G PRSAI+ Sbjct: 4 FPVLLGDIGGTNARFAVLPAPGAAVKLLPRTLTAQTPDPVGAIRIALEAYDGPAPRSAII 63 Query: 72 AVAGPIKDDEIPLTNCPWVIRPKAMIADLGFDDVLVVNDFEAQALAAASL--GRNDREPI 129 AVA + I LTN WVI +A+ L + V +VND+ A + A L + D PI Sbjct: 64 AVATRVDAPAIRLTNAHWVIDAEAIGKALDLERVTLVNDYTPVAASVAVLDEAKGDLAPI 123 Query: 130 GPLTETSLNSRVILGPGTGLGVGGLLYTHHTWFPVPGEGGHVDIGPRSDRDWQIFPHIER 189 G +RV+LGPGTGLG G L+ + E GH++ GP +D + I+PH+ER Sbjct: 124 GTFAPPKHGARVVLGPGTGLGAGALVPVEDRLAILATEAGHIEFGPTNDEETAIWPHLER 183 Query: 190 IEGRISGEQILCGRGILHLYNAICAADGIEPVWTDPADVTQHALKGNDPVCVETMTLFVT 249 + GRISGE +L G G+ + A+ A ++ +T P DV A +GN + V+ + F Sbjct: 184 VGGRISGEVVLSGPGLFRIAKALAAHRCVDCPFTIPNDVLAAAREGN-ALAVDALRHFSR 242 Query: 250 YLGRIAGDMALVFMARGGVFLSGGISQKIIPLLKSPVFRAAFEDKAPHTEMMKTIPTFVA 309 +LGR AGD+AL F + GGVF++GGI+ ++I +L+S FR AF+ KAPH + +P + Sbjct: 243 FLGRFAGDLALTFESSGGVFIAGGIAPRMIDILQSGDFRDAFDRKAPHDAWARKVPVYAI 302 Query: 310 IHPQAALSGLAAYARTPSSYGVKHEGRRWQ 339 ++P+ AL GLAA P + + +G WQ Sbjct: 303 VNPEPALEGLAAIVSNPQRFIFQSQG--WQ 330 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: 351 Number of extensions: 17 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: 332 Length adjustment: 28 Effective length of query: 312 Effective length of database: 304 Effective search space: 94848 Effective search space used: 94848 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