Align Glucose kinase (characterized, see rationale)
to candidate 16493 b2388 glucokinase (NCBI)
Query= uniprot:Q8P6M4 (344 letters) >FitnessBrowser__Keio:16493 Length = 321 Score = 179 bits (454), Expect = 9e-50 Identities = 112/313 (35%), Positives = 166/313 (53%), Gaps = 8/313 (2%) Query: 23 LAADVGGTHVRVGRVSHGADAPIELSQYRTYRCADHASLDAILADFLRDSRA-VDAVVIA 81 L DVGGT+ R+ + E+SQ +TY D+ SL+A++ +L + + V IA Sbjct: 6 LVGDVGGTNARLALCDIASG---EISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIA 62 Query: 82 SAGVALDDGRFISNNLPWTIAPRQLRDTLGVRAVHLVNDFEAVAYAAPQMEQRAVVQLSG 141 A D ++N+ W + +++ LG + ++NDF AV+ A P +++ ++Q G Sbjct: 63 IACPITGDWVAMTNHT-WAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGG 121 Query: 142 PTPRHAQPGGPILVVGPGTGLGAAVWINGPRQPTVLATEAGQVALASNDPDTAQVLRILA 201 P G PI V G GTGLG A ++ ++ L E G V A N + A +L IL Sbjct: 122 AEPVE---GKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILR 178 Query: 202 RDASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALHSDDALARRCLQLFC 261 + ++ E VLSGPGL NLY A+ + P + P DIT AL RR L LFC Sbjct: 179 AEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFC 238 Query: 262 ALLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAKGRMRPVLERIPVKL 321 ++G G++AL G GGV++AGGI+P +F AS FR F KGR + + IPV L Sbjct: 239 VIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYL 298 Query: 322 VEHGQLGVLGAAS 334 + H G+LG+ + Sbjct: 299 IVHDNPGLLGSGA 311 Lambda K H 0.321 0.136 0.410 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: 286 Number of extensions: 18 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: 344 Length of database: 321 Length adjustment: 28 Effective length of query: 316 Effective length of database: 293 Effective search space: 92588 Effective search space used: 92588 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