Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate H281DRAFT_00163 H281DRAFT_00163 glucokinase /transcriptional regulator, RpiR family
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__Burk376:H281DRAFT_00163 Length = 638 Score = 262 bits (670), Expect = 1e-74 Identities = 138/316 (43%), Positives = 191/316 (60%), Gaps = 4/316 (1%) Query: 6 LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKV-EVKDGCIAIA 64 L+ D+GGTNAR AL + GEI Y DYP + VI+ YL++ K+ V IAIA Sbjct: 22 LLADIGGTNARFAL-ETGPGEIGSVHVYPCADYPGVAEVIKKYLKDTKIGRVNHAAIAIA 80 Query: 65 CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124 P+ GD V+MTNH W+FSI ++ LGF L ++NDFTA++MA+P L +Q GG Sbjct: 81 NPVDGDQVSMTNHDWSFSIEATRRALGFDTLLVVNDFTALAMALPGLTDAQRVQVGGGTR 140 Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHV 184 I + G GTG+GV+ L+ D RW++L EGGH FAP E E I+L+ R + HV Sbjct: 141 RPNSVIGLLGPGTGMGVSGLIPADDRWIALGSEGGHATFAPADEREDIVLQYARKKWSHV 200 Query: 185 SAERVLSGPGLVNLYRAIVKAD-NRLPENLKPKDITERALADSCTDCRRALSLFCVIMGR 243 S ERV +GPG+ +YRA+ D R+ N+ +I +RAL ++ +FC I+G Sbjct: 201 SFERVAAGPGIEVIYRALAGRDKKRVAANVDTVEIVKRALEGEPL-AAESVDVFCGILGT 259 Query: 244 FGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDN 303 F GN+A+ LG GG++I GG+VPR EFF S FR FE KGRF+ Y+ ++P Y+I + Sbjct: 260 FAGNIAVTLGALGGIYIGGGVVPRLGEFFARSSFRKRFEAKGRFEAYLQNVPTYVITAEY 319 Query: 304 PGLLGSGAHLRQTLGH 319 P LG A L + L + Sbjct: 320 PAFLGVSAILAEQLSN 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: 578 Number of extensions: 25 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: 638 Length adjustment: 33 Effective length of query: 288 Effective length of database: 605 Effective search space: 174240 Effective search space used: 174240 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: 51 (24.3 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