Align glucokinase (EC 2.7.1.2) (characterized)
to candidate 7025639 Shewana3_2790 fructokinase (RefSeq)
Query= reanno::SB2B:6938110 (299 letters) >FitnessBrowser__ANA3:7025639 Length = 306 Score = 508 bits (1308), Expect = e-149 Identities = 242/306 (79%), Positives = 271/306 (88%), Gaps = 8/306 (2%) Query: 1 MMRMGVDLGGTKIELVALGEDGSELFRKRIATPREYQGTLNAVVTLVNEAEATLGTQGSL 60 M+RMG+DLGGTKIELVAL E+G+ELFRKRI TPR+YQGTLNA+V LVNEAEATLG +G++ Sbjct: 1 MIRMGIDLGGTKIELVALSEEGNELFRKRINTPRDYQGTLNAIVDLVNEAEATLGEKGTV 60 Query: 61 GIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAAA 120 G+GIPGVISPY+GLVKNANSTWINGHPLD +LG LL REVRVANDANCFAVSEAVDGAAA Sbjct: 61 GVGIPGVISPYSGLVKNANSTWINGHPLDVNLGELLGREVRVANDANCFAVSEAVDGAAA 120 Query: 121 GKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLPWMRPDEFNTTECFCGNKDC 180 GK VVFG I+GTGCGAG+A +G+VH GGNGIGGEWGHNPLPWM +EFNTT CFCGN DC Sbjct: 121 GKSVVFGVIIGTGCGAGVAINGKVHAGGNGIGGEWGHNPLPWMTKEEFNTTRCFCGNPDC 180 Query: 181 IETFVSGTGFVRDFRNS--------GGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARS 232 IETF+SGTGFVRD+ + A++G EIM+LVDAGDE+A FDRY+DRLARS Sbjct: 181 IETFISGTGFVRDYNEALSRAVNVQAAPAKSGTEIMALVDAGDEMAIAAFDRYMDRLARS 240 Query: 233 LAHVINMLDPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNLYGCSSGVRGA 292 LAHVINMLDPDAIVLGGGMSN++A Y RLPA+L +YVVGRECRTPVVQNLYGCSSGVRGA Sbjct: 241 LAHVINMLDPDAIVLGGGMSNIEATYPRLPALLTRYVVGRECRTPVVQNLYGCSSGVRGA 300 Query: 293 AWLWEK 298 AWLWEK Sbjct: 301 AWLWEK 306 Lambda K H 0.320 0.139 0.429 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: 417 Number of extensions: 14 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: 299 Length of database: 306 Length adjustment: 27 Effective length of query: 272 Effective length of database: 279 Effective search space: 75888 Effective search space used: 75888 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 (21.8 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