Align glucokinase (EC 2.7.1.2) (characterized)
to candidate BWI76_RS22415 BWI76_RS22415 transcriptional regulator
Query= reanno::SB2B:6937235 (310 letters) >FitnessBrowser__Koxy:BWI76_RS22415 Length = 304 Score = 277 bits (709), Expect = 2e-79 Identities = 141/297 (47%), Positives = 192/297 (64%), Gaps = 6/297 (2%) Query: 1 MYRSGIDLGGTKIELVTLNEKGEEVFRKRVPTPKD-YRATLEAVAGLVHDSEKETGQVSS 59 M G+D+GGTK+E V LN GE V+R+R PT K+ Y A ++ + GL+ + + + Sbjct: 1 MLHLGLDIGGTKMEAVLLNAAGECVYRQRRPTHKESYDAFMQQLLGLIESVRAWSERPFT 60 Query: 60 VGIGIPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGG 119 +GIG+PG + +G +KN N + LNG + DL LG+ V +ANDA+CF +SE+VDG G Sbjct: 61 LGIGLPGAIDPQSGLIKNCNCLVLNGHDLRHDLMRELGQSVWMANDADCFTLSEAVDGAG 120 Query: 120 AGKTLVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLPWMTADEFNSTR-CFCGNA 178 AG T VFG I+GTGCG G+A+N ++ G N I GEWGHNPLP + + C+CG Sbjct: 121 AGATTVFGVIIGTGCGGGVAVNQRLLSGPNAIAGEWGHNPLPGYRPERDGPAQPCYCGKE 180 Query: 179 DCIETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVIN 238 +CIE+F+SGTGF R + G A I+A G PLA A + FID AR+LA VIN Sbjct: 181 NCIESFISGTGFARRY----GAQARSEAIIAAAQNGAPLALAHWRHFIDAFARSLASVIN 236 Query: 239 LLDPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWL 295 +LDP VIVLGGG+SN+ +IYE LP+ + Y+ C T++ + G +SGVRGAAWL Sbjct: 237 ILDPQVIVLGGGLSNVGQIYEQLPSAIVPYLFSDSCRTQIKQARFGDASGVRGAAWL 293 Lambda K H 0.318 0.138 0.424 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: 318 Number of extensions: 20 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: 310 Length of database: 304 Length adjustment: 27 Effective length of query: 283 Effective length of database: 277 Effective search space: 78391 Effective search space used: 78391 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 (21.6 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