Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_027722474.1 H589_RS0113290 glucokinase
Query= curated2:Q1QFN5 (320 letters) >NCBI__GCF_000425265.1:WP_027722474.1 Length = 316 Score = 105 bits (262), Expect = 1e-27 Identities = 98/315 (31%), Positives = 137/315 (43%), Gaps = 26/315 (8%) Query: 13 DIGGTYARFAVAERGK-----YSELQHLSVSKYAALKDALGEYLAALPRDLRPTRG---A 64 DIGGT +RFA + +E LS SK A + L + LA P Sbjct: 8 DIGGTNSRFAAFDTDSDGHITMNETVWLS-SKEAKSFEHLLDMLAHSDFPYSPQEFDIVV 66 Query: 65 LAVAGPV-SGDEVKLTNLNWSFSITALKADLGMSSLVVVNDFAATAMSVPYLPEADCYPI 123 LA+AGPV G +TN++W + G +++NDFAA A + C I Sbjct: 67 LALAGPVIRGVYCNVTNVDWDVDFSEGYEKYGFKKAILINDFAAQAYACRTSAVDGCKVI 126 Query: 124 GPPQSKTSGPVGVIGPGTGLGVSALVP-DAGRWILLPGEGGHSTLPPATQAE---SLIVE 179 +G VGVIG GTGLG ALVP ++ +P E GH + P T AE V+ Sbjct: 127 HDVDISPTGAVGVIGAGTGLGHCALVPVPPAGFVSVPSEAGHISFPFQTHAELDFCGFVK 186 Query: 180 VLRTHWPHVSAERALSGAGLVNLYQALCSIEGKRPDPLSPADVTDRAMRGSDPTCVKAFE 239 LR + + L+G GL L+ L + +SP D++ +G + E Sbjct: 187 ELR-GISYCYGDEVLTGRGLNVLHYYLTG------EDISPQDISKEMAKGG-----RTLE 234 Query: 240 VFCSMLGTVAGDLALTIGATGGIYIAGGILLRFKEAFASSPFRDRFEDKGRFQDYLRRIP 299 + + AL+I ATGG+YI+GGI+ + F F D D L+RIP Sbjct: 235 WYAKFTARCCRNYALSICATGGLYISGGIIAKNPFVVDHPLFMKEFLDSSSMHDLLKRIP 294 Query: 300 TLLILEESPALLGLA 314 L + L G A Sbjct: 295 VFLNDNQESGLYGAA 309 Lambda K H 0.318 0.137 0.408 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: 231 Number of extensions: 17 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: 320 Length of database: 316 Length adjustment: 27 Effective length of query: 293 Effective length of database: 289 Effective search space: 84677 Effective search space used: 84677 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 24 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