Align Glucose kinase (characterized, see rationale)
to candidate GFF2219 HP15_2173 glucokinase
Query= uniprot:Q8P6S9 (338 letters) >FitnessBrowser__Marino:GFF2219 Length = 321 Score = 171 bits (434), Expect = 2e-47 Identities = 103/312 (33%), Positives = 154/312 (49%), Gaps = 6/312 (1%) Query: 19 VAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAELSCAPVRRG 78 + D+GGT+ R AL + + + +L C +Y L + + + A + + V Sbjct: 8 LVGDIGGTNARFALVEQGTVQPRAIKILP-----CGEYANLDDAVRDYLARVGVSEVDGA 62 Query: 79 VIASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYMTGNQVMQ 138 +A A + +V N W+ E++R Q G ++NDF A+A ++ + ++ Sbjct: 63 CLAVAS-PVRGTQVRMTNNHWLFDTEEVRAQFGWSRFKVINDFTAMALGVPHVANDHLVH 121 Query: 139 LSGPAQGAPGPALVLGPGTGLGAALWIPNGGNSVVLPTEAGHAALAAASDLEVALLQELR 198 + G + P LV+GPGTGLG + +P V L TE GH A D E+A+L+ L+ Sbjct: 122 VCGGPGDSRRPRLVMGPGTGLGVSGLVPIEHGWVPLMTEGGHVDFAPTDDAEMAVLRILK 181 Query: 199 RTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAHEALQTFC 258 V+ E L G GLL LY A A ++ A P +TAAA+ D LA L FC Sbjct: 182 ARFGRVSVERILCGQGLLNLYQAHAEIQGVAAPLDAPEKITAAAVENTDRLARHTLSHFC 241 Query: 259 GFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALEQVPVRI 318 +G V G+ +L G GV+L GG LP+ +F S F DKG +RP LE PV + Sbjct: 242 EILGRVAGNGVLTLGSTGGVFLCGGILPRFLEFFLESPFRNGFEDKGRMRPLLEFTPVYV 301 Query: 319 VEHGQLGVIGAA 330 V G++GAA Sbjct: 302 VTEPYTGLLGAA 313 Lambda K H 0.321 0.136 0.407 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: 244 Number of extensions: 11 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: 338 Length of database: 321 Length adjustment: 28 Effective length of query: 310 Effective length of database: 293 Effective search space: 90830 Effective search space used: 90830 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 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