Align LacI family transcriptional regulator, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate H281DRAFT_02713 H281DRAFT_02713 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= TCDB::G4FGN5 (343 letters) >FitnessBrowser__Burk376:H281DRAFT_02713 Length = 313 Score = 138 bits (347), Expect = 2e-37 Identities = 103/325 (31%), Positives = 154/325 (47%), Gaps = 53/325 (16%) Query: 20 SEDMTILLAPKSLNNPYWFAVENGMKDAAEKLGIKAIFDAPVEADAAKQAEKILSYIVKG 79 ++D+++ + PK + P++ G K AA K G+K + P + Q + I I + Sbjct: 28 AKDISVAVIPK-VAVPFFDDCNKGAKTAAGKAGVKYQWVVPQNTQGSTQVQIIEDLISRH 86 Query: 80 VDGIGISPNDPEGIKVVVKRALDKGIPVIMFDSDSPDSGRYAYIGTNNYNAGYEAGKLMA 139 VDGI IS N+P+ ++ V+KRA GI V+ +DSDSP SGR YIGTNN AG + M Sbjct: 87 VDGIAISVNEPKSVESVMKRAEQSGIKVLTYDSDSPRSGRSMYIGTNNEQAGATMAETMG 146 Query: 140 QLIEKYKAEKKTIRLAILTGGLAALNLNERIRGFKDALEDYSKRSGKEIVYVADPFPCDD 199 KA +AI+TG L A+NLNERI G K L Y + + + DD Sbjct: 147 ------KALNGQGEVAIITGQLGAVNLNERIAGIKKGLAKYPG------IKIVETQGTDD 194 Query: 200 DSAKAIQIIRDVTRKYTDLDGWFMSGGWPLFAPKETVISALGGPERMK------------ 247 D A+ + ++ R + L G F +S +GGP K Sbjct: 195 DLARGVSVVETTLRAHPQLKGIF-------------GVSQVGGPAVAKVLNTKEFGTMKG 241 Query: 248 DLLVVGFDTLLPELELVKAGAVKGLVGQRPYDMGYLSVLVLYNMAKIGVENTLKMLPKVV 307 L V+ FD L L+ +K G ++G++ QRP MG L+V + L + Sbjct: 242 KLEVLAFDDLPDTLKGLKEGYIQGIMVQRPVTMGSLAV---------------EHLVAQI 286 Query: 308 KEDGTVDYIIDTGVDIVTEENVDQF 332 + IDTGV +VT++N+ + Sbjct: 287 QGQEAQPKDIDTGVTVVTKDNMTSY 311 Lambda K H 0.318 0.139 0.398 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: 251 Number of extensions: 15 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: 343 Length of database: 313 Length adjustment: 28 Effective length of query: 315 Effective length of database: 285 Effective search space: 89775 Effective search space used: 89775 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: 49 (23.5 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