Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate GFF2219 HP15_2173 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__Marino:GFF2219 Length = 321 Score = 254 bits (649), Expect = 2e-72 Identities = 136/313 (43%), Positives = 185/313 (59%), Gaps = 1/313 (0%) Query: 2 TKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDG-C 60 T Y+LVGD+GGTNAR AL + + + K +Y +L+ +R YL V DG C Sbjct: 4 THYSLVGDIGGTNARFALVEQGTVQPRAIKILPCGEYANLDDAVRDYLARVGVSEVDGAC 63 Query: 61 IAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFG 120 +A+A P+ G V MTN+ W F E++ G+S ++INDFTA+++ +P + +HL+ Sbjct: 64 LAVASPVRGTQVRMTNNHWLFDTEEVRAQFGWSRFKVINDFTAMALGVPHVANDHLVHVC 123 Query: 121 GAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAE 180 G +P V G GTGLGV+ LV ++ WV L EGGHVDFAP + E +L IL+A Sbjct: 124 GGPGDSRRPRLVMGPGTGLGVSGLVPIEHGWVPLMTEGGHVDFAPTDDAEMAVLRILKAR 183 Query: 181 IGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI 240 G VS ER+L G GL+NLY+A + P+ IT A+ ++ R LS FC I Sbjct: 184 FGRVSVERILCGQGLLNLYQAHAEIQGVAAPLDAPEKITAAAVENTDRLARHTLSHFCEI 243 Query: 241 MGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIV 300 +GR GN L LG+ GGVF+ GGI+PRFLEFF S FR FEDKGR + + PVY++ Sbjct: 244 LGRVAGNGVLTLGSTGGVFLCGGILPRFLEFFLESPFRNGFEDKGRMRPLLEFTPVYVVT 303 Query: 301 HDNPGLLGSGAHL 313 GLLG+ L Sbjct: 304 EPYTGLLGAAEAL 316 Lambda K H 0.322 0.141 0.426 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: 320 Number of extensions: 13 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: 321 Length of database: 321 Length adjustment: 28 Effective length of query: 293 Effective length of database: 293 Effective search space: 85849 Effective search space used: 85849 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: 48 (23.1 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