Align Putative beta-xyloside ABC transporter, permease component, 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 WP_085637954.1 MGEO_RS12240 ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >NCBI__GCF_002115805.1:WP_085637954.1 Length = 362 Score = 199 bits (506), Expect = 8e-56 Identities = 122/339 (35%), Positives = 184/339 (54%), Gaps = 42/339 (12%) Query: 10 EAGIFLILIAIVVFLGV------------------TTRE--FLTVENIFTVILNVSFIAI 49 EA +F+ L+ I++ T R+ L + I VIL VS I I Sbjct: 24 EANVFIALVLIILIFEALGQILPYMNGQSMLFDFNTNRDGTILNIARIKIVILQVSIIGI 83 Query: 50 MSFGMTMVIITSGIDLSVGSILGAAS-VVMGLLMDEK----------------GLSPFLS 92 ++ G+T VII+ GIDLS G ++GAA+ +VM E L + Sbjct: 84 IALGVTQVIISGGIDLSSGPLVGAAAMIVMSFAQTELVNGNPNPKAVFGPWSFDLPVIIP 143 Query: 93 VVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVMSGGWPISPFPESFTVH 152 +++GLA G G NG I R+ PFI+TLGM + RG+A + G P+S E + Sbjct: 144 ILVGLAFGALIGAINGTFIALTRIPPFIATLGMFLICRGIAQWWTKGQPVSFPTEQYAAL 203 Query: 153 GQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIGGNMEASKLVGIKTDRILILVY 212 G GM+ PV++ ++ + + +K+TV G+ YAIG N +A+++ GI R ILVY Sbjct: 204 GAGMM-----PVVWFVLLAAVFFVIMKFTVYGKHTYAIGSNEDAARMSGINVKRHKILVY 258 Query: 213 TINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVIGGTSLSGGEGTILGAFLGAVI 272 I G LAAFA +L++ AQ GQ YEL IA VIGG SL+GG G+I+G LGA++ Sbjct: 259 MIAGMLAAFAAIVLSSKNLTAQAGMGQFYELYAIAMAVIGGVSLTGGRGSIVGTVLGAMV 318 Query: 273 MGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIRRAK 311 GV+++G + + +F+Q + +G +II A+ +DQ R+ + Sbjct: 319 FGVIQSGFTFIKLDAFYQLMAMGAIIISAVVLDQWRQQR 357 Lambda K H 0.328 0.145 0.421 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: 309 Number of extensions: 21 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: 313 Length of database: 362 Length adjustment: 28 Effective length of query: 285 Effective length of database: 334 Effective search space: 95190 Effective search space used: 95190 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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