Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_047007751.1 AAW01_RS12295 glucokinase
Query= curated2:P21908 (324 letters) >NCBI__GCF_001010925.1:WP_047007751.1 Length = 324 Score = 365 bits (937), Expect = e-106 Identities = 175/323 (54%), Positives = 236/323 (73%), Gaps = 1/323 (0%) Query: 1 MEIVAIDIGGTHARFSIAEVSNGRVLSLGEETTFKTAEHASLQLAWERFGEKLGRPLPRA 60 M++V +DIGGTHARF+IA ++ +++ E T T +HAS Q AWE + + G +P Sbjct: 1 MQLVTVDIGGTHARFAIATHADDGSITMDEPVTLHTDDHASFQTAWEDYRAQKGGDIPSR 60 Query: 61 AAIAWAGPVHGEVLKLTNNPWVLRPATLNEKLDIDTHVLINDFGAVAHAVAHMDSSYLDH 120 A+A AGPV GEV++ TNNPW++RPA + EKL +D+ ++NDF AVAHAVA H Sbjct: 61 VAMAIAGPVGGEVIRFTNNPWIIRPALVKEKLGVDSFKIVNDFEAVAHAVARAGEDEYLH 120 Query: 121 ICGPDEALPSDGVITILGPGTGLGVAHLLR-TEGRYFVIETEGGHIDFAPLDRLEDKILA 179 + GP+ LP G +T++GPGTGLGVAHL R +G Y V TEGGHIDFAPLD +ED ILA Sbjct: 121 LTGPEGPLPPTGRLTVMGPGTGLGVAHLYREADGTYRVSATEGGHIDFAPLDSIEDAILA 180 Query: 180 RLRERFRRVSIERIISGPGLGNIYEALAAIEGVPFSLLDDIKLWQMALEGKDNLAEAALD 239 RLR+R RVS+ER+++GP + +IY LA++E LDD+++W + G+D+LA AA+D Sbjct: 181 RLRKRHTRVSVERVVAGPAISDIYHTLASLERKSVPELDDVEIWTRGMNGEDSLAAAAVD 240 Query: 240 RFCLSLGAIAGDLALAQGATSVVIGGGVGLRIASHLPESGFRQRFVSKGRFERVMSKIPV 299 RFCLSLG++AGD+ALA GA +VVI GG+G R+ HLP+SGF +RF +KGRF +M+ +PV Sbjct: 241 RFCLSLGSVAGDMALAHGAKAVVIAGGLGYRLRDHLPKSGFAERFRAKGRFAGLMAGLPV 300 Query: 300 KLITYPQPGLLGAAAAYANKYSE 322 KLIT+PQPGL GAAAAY K+ + Sbjct: 301 KLITHPQPGLFGAAAAYCQKFGD 323 Lambda K H 0.320 0.139 0.411 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: 423 Number of extensions: 23 Number of successful extensions: 2 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: 324 Length of database: 324 Length adjustment: 28 Effective length of query: 296 Effective length of database: 296 Effective search space: 87616 Effective search space used: 87616 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 (21.8 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