Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate Synpcc7942_0221 Synpcc7942_0221 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__SynE:Synpcc7942_0221 Length = 345 Score = 157 bits (396), Expect = 5e-43 Identities = 109/337 (32%), Positives = 165/337 (48%), Gaps = 38/337 (11%) Query: 6 LVGDVGGTNARLALCDIASG----EISQAKTYSGLDYPSLEAVIRVYLEEH-KVEVKD-- 58 L GD+GGT L L IAS E +++ YP L +++ +L EV+ Sbjct: 5 LAGDIGGTKTNLMLA-IASDCDRLEPLHQASFASAAYPDLVPMVQEFLAAAPSAEVRSPV 63 Query: 59 -GCIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEH-- 115 C IA P+ +TN W S A + K LG + + +INDF A++ +P L E Sbjct: 64 VACFGIAGPVVHGTAKLTNLPWQLSEARLAKELGIAQVALINDFAAIAYGLPGLTAEDQV 123 Query: 116 LIQFGGAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILE 175 ++Q G A+P PIA+ GAGTGLG ++ + EG H DFAP +E E+ +L Sbjct: 124 VVQVGEADPAA--PIAILGAGTGLGEGFIIPTAQGRQVFGSEGSHADFAPQTELESELLH 181 Query: 176 ILR--AEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKP------------------ 215 LR I H+S ERV+SG G+ +Y + +R P+ P Sbjct: 182 FLRNFYAIEHISVERVVSGQGIAAIYAFL---RDRHPDQENPALGAIASAWQTGGDQAPD 238 Query: 216 --KDITERALADSCTDCRRALSLFCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFK 273 +++ AL+D +A+ +F G GNLAL L ++GGV++AGGI + L Sbjct: 239 LAAAVSQAALSDRDPLALQAMQIFVSAYGAEAGNLALKLLSYGGVYVAGGIAGKILPLLT 298 Query: 274 ASGFRAAFEDKGRFKEYVHDIPVYLIVHDNPGLLGSG 310 F AF+ KGR K + +P+ ++ + GL+G+G Sbjct: 299 DGTFLQAFQAKGRVKGLLTRMPITIVTNHEVGLIGAG 335 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: 275 Number of extensions: 15 Number of successful extensions: 4 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