Align glucokinase (EC 2.7.1.2) (characterized)
to candidate BWI76_RS27555 BWI76_RS27555 putative sugar kinase/transcriptional regulator, ATPase domain protein
Query= reanno::SB2B:6937235 (310 letters) >FitnessBrowser__Koxy:BWI76_RS27555 Length = 310 Score = 225 bits (573), Expect = 1e-63 Identities = 127/296 (42%), Positives = 177/296 (59%), Gaps = 8/296 (2%) Query: 5 GIDLGGTKIELVTLNEKGEEVFRKRVPTPKDYR----ATLEAVAGLVHDSEKETGQVSSV 60 G+D+GG+KI V ++E+G E R RV T K R ATL + + D E Q ++ Sbjct: 5 GLDIGGSKIAAVVMDEQGHEWRRFRVETRKQTRQQFIATLVELITAIGD---ELAQPLAI 61 Query: 61 GIGIPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGA 120 GI +PG +S +G+++N+N +NG + +L LG+ V +AND NCFA+SE+ DG GA Sbjct: 62 GIALPGSISPQSGKIRNANIQVINGCRLQDELEQRLGQSVVLANDGNCFALSEACDGAGA 121 Query: 121 GKTLVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLP-WMTADEFNSTRCFCGNAD 179 +LVFG LGTGCG GIA+N ++ G +GI E GH LP + ++ RC+CG + Sbjct: 122 DYSLVFGMTLGTGCGGGIALNRQIFPGASGIAAECGHITLPGYQEVNDGPPARCYCGKYN 181 Query: 180 CIETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVINL 239 C+E+F+SGTG +R EA S I+A +GE A RF +LAR LA V+NL Sbjct: 182 CVESFISGTGLSARYRLLTQEALSSQAIIARALEGEHAACEQVLRFRQQLARTLATVVNL 241 Query: 240 LDPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWL 295 +DP VI+LGGG+SN+ + L A + V T +V HG SSG+RGAAWL Sbjct: 242 IDPGVIILGGGLSNVALLVNDLEADVAPLVFTDHFITPIVPARHGDSSGMRGAAWL 297 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: 291 Number of extensions: 12 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: 310 Length of database: 310 Length adjustment: 27 Effective length of query: 283 Effective length of database: 283 Effective search space: 80089 Effective search space used: 80089 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