Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate GFF4431 PS417_22685 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__WCS417:GFF4431 Length = 318 Score = 216 bits (549), Expect = 8e-61 Identities = 128/317 (40%), Positives = 173/317 (54%), Gaps = 7/317 (2%) Query: 3 KYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKD---G 59 K ALVGD+GGTNAR AL E+ + ++ D+ S E I+VYL+E +E+ D Sbjct: 2 KLALVGDIGGTNARFALW--RDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAV 59 Query: 60 CIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQF 119 C+++A P++GD TN+ W S K L L ++NDF+A+++ + LK + Sbjct: 60 CLSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVV 119 Query: 120 GGAEPVEGKPIAVYGAGTGLGVAHLVHVDK-RWVSLPGEGGHVDFAPNSEEEAIILEILR 178 P +P V G GTGLGV L+ + R+ +LPGEGGHVD +S E + + + Sbjct: 120 CEGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIY 179 Query: 179 AEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFC 238 EIGHVSAE LSG GL LYRAI D P P+ IT LA L F Sbjct: 180 TEIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPV-AMEVLDQFS 238 Query: 239 VIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYL 298 + +GR GN L G GGV+I GG++PRF +FF SGF +F DKG +Y IPV+L Sbjct: 239 IWLGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWL 298 Query: 299 IVHDNPGLLGSGAHLRQ 315 + GL G+G L Q Sbjct: 299 VTAPYSGLTGAGVALEQ 315 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: 323 Number of extensions: 19 Number of successful extensions: 4 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: 318 Length adjustment: 28 Effective length of query: 293 Effective length of database: 290 Effective search space: 84970 Effective search space used: 84970 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