Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate SMc02835 SMc02835 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__Smeli:SMc02835 Length = 339 Score = 193 bits (490), Expect = 6e-54 Identities = 112/310 (36%), Positives = 161/310 (51%), Gaps = 1/310 (0%) Query: 6 LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLE-AVIRVYLEEHKVEVKDGCIAIA 64 L+GD+GGTNAR AL A GE Q D+ ++E A+ + L++ V+ + +A+A Sbjct: 14 LIGDIGGTNARFALLTDAYGEPKQLAPIRTGDFATIEEAMQKGILDKTSVQPRSAILAVA 73 Query: 65 CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124 PI GD + +TN W +M LG + +INDF A ++AI + ++Q GG Sbjct: 74 GPIKGDEIPLTNAGWVIRPKDMLAGLGLEDVLVINDFEAQALAIAAPADQDVVQIGGGAV 133 Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHV 184 V G GTGLGVA LV+ W+ +PGEGGHVD P +E + I L G + Sbjct: 134 RPFHSRVVLGPGTGLGVAGLVYAQHTWIPVPGEGGHVDIGPRTERDFRIWPFLEPIEGRM 193 Query: 185 SAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRF 244 + E++L G G++NLYRA+ A+ +T AL+ + +SLF +GR Sbjct: 194 AGEQILCGRGIMNLYRAVCAANGEEAVLADQAAVTTSALSGADAAAVETVSLFATYLGRV 253 Query: 245 GGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNP 304 G++AL GGVF+AGGI + L FRAAFEDK + IP + ++H Sbjct: 254 AGDMALIFMARGGVFLAGGISQKILPALTKPEFRAAFEDKAPHSALMRTIPTFAVIHPMA 313 Query: 305 GLLGSGAHLR 314 L G A R Sbjct: 314 ALSGLAAFAR 323 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: 327 Number of extensions: 15 Number of successful extensions: 2 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