Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate HSERO_RS17870 HSERO_RS17870 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__HerbieS:HSERO_RS17870 Length = 333 Score = 245 bits (625), Expect = 1e-69 Identities = 133/313 (42%), Positives = 175/313 (55%), Gaps = 2/313 (0%) Query: 6 LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLE-EHKVEVKDGCIAIA 64 L+ D+GGTNAR AL + G I Q + G DY ++ YL+ V+ +AIA Sbjct: 18 LLADIGGTNARFAL-ETGPGRIEQVQILRGADYGEFTDAVQAYLKLAGHPPVRHAVVAIA 76 Query: 65 CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124 P+ GD + MTNH WAFSI ++ LGF L ++NDFTA+SMA+P L+ + L Q GG P Sbjct: 77 NPVQGDQIKMTNHDWAFSIEAARQLLGFELLLVVNDFTALSMAVPQLRADELQQVGGGAP 136 Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHV 184 G PI + GAGTGLGV L+H D W+ L EGGH FAP EA +L HV Sbjct: 137 KPGAPIGLVGAGTGLGVGGLLHADGHWLPLASEGGHAAFAPADPREAAVLAYAWQFHEHV 196 Query: 185 SAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRF 244 SAER++SGPGL ++RA++ D L I E A C+ L+LFC ++G Sbjct: 197 SAERLVSGPGLELIHRALLAIDGHPAAELSAAQIVEGARQHGDALCQETLALFCSMLGTV 256 Query: 245 GGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNP 304 +LAL LG GG++I G+VP ++F S FRA FE+KGR IP Y+I + P Sbjct: 257 AADLALTLGALGGIYIGVGVVPHLGDYFARSPFRARFENKGRMSVLTKAIPTYVITAEYP 316 Query: 305 GLLGSGAHLRQTL 317 G A L L Sbjct: 317 AFTGVSAILADRL 329 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: 358 Number of extensions: 15 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: 333 Length adjustment: 28 Effective length of query: 293 Effective length of database: 305 Effective search space: 89365 Effective search space used: 89365 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