Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate 5208927 Shew_1428 fructokinase (RefSeq)
Query= BRENDA::Q8R8N4 (312 letters) >FitnessBrowser__PV4:5208927 Length = 296 Score = 127 bits (319), Expect = 3e-34 Identities = 93/317 (29%), Positives = 150/317 (47%), Gaps = 29/317 (9%) Query: 1 MRIGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVK 60 MR+GVDLGGT I + + E GK + PT E Y+A I L E +G Sbjct: 2 MRMGVDLGGTKIELVALSEAGKELFRKRIPTPRE--YKATLDAIEALVNEAESTLG---- 55 Query: 61 DVKSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDANVAALAEAT 120 ++G+G+PGV G+V A + + PL ++ ++ + + NDAN A++EA Sbjct: 56 QKGTVGVGIPGVISPFSGLVKNANSTWINGHPLDLDLGARLEREVRVANDANCFAVSEAV 115 Query: 121 FGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVI------GDNGIRCNC 174 GA G + +GTG G G ++GK++ G + E GH + N C C Sbjct: 116 DGAAAGKGLVFGVIIGTGCGGGIAINGKVHGGGNGIGGEWGHNPLPWMTPDEFNSTECFC 175 Query: 175 GKIGCFETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALK 234 G C ET+ S T +R+ K A P+ + + +Q + A Sbjct: 176 GNKDCIETFISGTGFVRDYKAAGGDAPSGI---------------EIARRMEQGEALATA 220 Query: 235 IFEEYVKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADI 294 FE Y+ LA + ++IN+ DP++I+LGGGV+N + + L + +++ +L E + Sbjct: 221 AFERYIDRLARSLAHMINMLDPDIIVLGGGVSNI-EAIYPRLPEALSKYVLGGECRTPVV 279 Query: 295 RKAELGNDAGIIGAAIL 311 + G +G+ GAA L Sbjct: 280 QNM-YGGSSGVRGAAWL 295 Lambda K H 0.318 0.140 0.397 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: 322 Number of extensions: 14 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: 312 Length of database: 296 Length adjustment: 27 Effective length of query: 285 Effective length of database: 269 Effective search space: 76665 Effective search space used: 76665 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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