Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate N515DRAFT_4210 N515DRAFT_4210 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__Dyella79:N515DRAFT_4210 Length = 339 Score = 205 bits (522), Expect = 1e-57 Identities = 122/315 (38%), Positives = 167/315 (53%), Gaps = 9/315 (2%) Query: 6 LVGDVGGTNARLALCDIASGE---ISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIA 62 L+ D+GGTN R AL D A + + + Y D+PS+ IR Y + + IA Sbjct: 10 LLADLGGTNVRFALADPALPQPLLLDSVRRYRVKDFPSMADTIRQYFADSGLSAGRAVIA 69 Query: 63 IACPIT-GDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGG 121 A I G+ V +TN+ W S + +L F + +INDF A MA+P+L L G Sbjct: 70 AAGRIVDGETVKVTNNPWQVSAHGLAADLKFDSVRLINDFAAQGMAVPLLACNELQPVGA 129 Query: 122 AEPVE-----GKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEI 176 +P + + V G GTGLGVA L+ D RW L EGGH FA ++ E+ IL Sbjct: 130 PQPPKIGAHHSQTFVVVGPGTGLGVAGLLLRDGRWTVLETEGGHAGFAAHTAEDVEILHR 189 Query: 177 LRAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSL 236 L A G VS ER++ G GLVNLY A+ + E P+DIT RA A + C R + Sbjct: 190 LNARFGRVSNERMICGNGLVNLYLALADIEGLKAEEYTPEDITTRANAGTDPLCVRTVET 249 Query: 237 FCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPV 296 I G G+L L+LG + GVF+ GG++P L + + GFR FE KGRFKE + +P Sbjct: 250 LAGIFGSVAGDLVLSLGGWDGVFLTGGVLPILLPWLQHGGFRERFESKGRFKETMEQVPT 309 Query: 297 YLIVHDNPGLLGSGA 311 ++H GLLG+ A Sbjct: 310 VAMMHAETGLLGAAA 324 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: 293 Number of extensions: 12 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: 339 Length adjustment: 28 Effective length of query: 293 Effective length of database: 311 Effective search space: 91123 Effective search space used: 91123 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