Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_057506803.1 ABB28_RS00795 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >NCBI__GCF_001431535.1:WP_057506803.1 Length = 341 Score = 142 bits (358), Expect = 1e-38 Identities = 99/309 (32%), Positives = 146/309 (47%), Gaps = 5/309 (1%) Query: 6 LVGDVGGTNARLALCD--IASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIAI 63 +V DVGGT ARLA + I + Y YPSL A++ + + +AI Sbjct: 29 IVADVGGTFARLAWSHGGAHAPRIDGFRRYRCAQYPSLAAILADFAATATPQPAAAVVAI 88 Query: 64 ACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQF-GGA 122 A + GD + N W S+ ++ G L++INDF AV++AIP ++ + L+ G A Sbjct: 89 AGLLQGDTLVNANLPWPVSVDATRQQAGLRSLQLINDFEAVALAIPHVRSDALVALHGSA 148 Query: 123 EPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIG 182 +P P V G GTGLG A L D L E GH + + E +L +L Sbjct: 149 DPATAWPALVLGPGTGLGAA-LRFADGARPVLASEVGHSALSAGTALELDVLRLLLQRWD 207 Query: 183 HVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMG 242 HV ERVLSG GL+NLY+ + + + + A R + +FC +G Sbjct: 208 HVDNERVLSGTGLLNLYQCLCQLRGASAHCDDTEALLAAAHRGDDPLARETVDVFCGWLG 267 Query: 243 RFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHD 302 F G+LA+ G V++AGG+ F S F A F +KG + +PV+ + H Sbjct: 268 SFVGDLAITFGA-RAVYLAGGVSAHIAPFLPDSPFVARFLNKGVLGSVLQQVPVWRVEHG 326 Query: 303 NPGLLGSGA 311 G+LG+ A Sbjct: 327 ELGVLGAAA 335 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: 280 Number of extensions: 15 Number of successful extensions: 6 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: 341 Length adjustment: 28 Effective length of query: 293 Effective length of database: 313 Effective search space: 91709 Effective search space used: 91709 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