Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate RR42_RS37395 RR42_RS37395 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__Cup4G11:RR42_RS37395 Length = 345 Score = 220 bits (560), Expect = 4e-62 Identities = 130/320 (40%), Positives = 180/320 (56%), Gaps = 8/320 (2%) Query: 6 LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYL---EEHKVEVKDGCIA 62 L+GDVGGTN R AL + A I D+PSLEA ++ YL + I Sbjct: 7 LLGDVGGTNVRFAL-ETAPQRIGPVTALKVADFPSLEAAVQHYLGGLPPGSARPRHAAIG 65 Query: 63 IACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGA 122 +A P+TGD V +TNH WAFSI++M+++LG L INDFTA+++ +P L L Sbjct: 66 LANPVTGDRVKLTNHAWAFSISQMQRSLGLDLLLAINDFTALALGLPHLGAHDLTLLRQG 125 Query: 123 EPVEGKPIAVYGAGTGLGVAHLVHVDKR-WVSLPGEGGHVDFAPNSEEEAIILEILRAEI 181 V G P+A+ G GTGLGV+ LV V+L GEGGH++ P +E+E + Sbjct: 126 VAVTGAPLALVGPGTGLGVSGLVPARSGPAVALAGEGGHIELMPQTEDEWTAWRAAQQAF 185 Query: 182 GHVSAERVLSGPGLVNLYRAIVKADNRLP--ENLKPKDITERALADSCTDCRRALSLFCV 239 G VSAER+LSG GL +L A + A+ P L+P ++TE A+ C RAL++FC Sbjct: 186 GRVSAERLLSGMGL-SLTHAALHAETGTPLARQLEPAEVTEGAIHRHDPLCERALAVFCG 244 Query: 240 IMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLI 299 ++G ++AL LG GGV++ GGIVPRF+ + S F A F KGR Y+ +PVY+I Sbjct: 245 LLGSVAADIALVLGARGGVYLGGGIVPRFVPALRNSAFNARFTAKGRLSAYLESLPVYVI 304 Query: 300 VHDNPGLLGSGAHLRQTLGH 319 P L G L + + H Sbjct: 305 NAQYPALPGLAQALEEAITH 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: 361 Number of extensions: 20 Number of successful extensions: 5 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: 345 Length adjustment: 28 Effective length of query: 293 Effective length of database: 317 Effective search space: 92881 Effective search space used: 92881 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