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_078430749.1 BK574_RS01735 ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >NCBI__GCF_002019605.1:WP_078430749.1 Length = 321 Score = 173 bits (438), Expect = 6e-48 Identities = 97/289 (33%), Positives = 158/289 (54%), Gaps = 2/289 (0%) Query: 20 IVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAASVVMG 79 I++F ++ F + +N + +SF+ I++ G T+V+ DLS+G++ V+ Sbjct: 29 IIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVKEFDLSIGAMASLGGVLSA 88 Query: 80 LLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVMSGG 139 LL G +++ + VG G NG ++TK ++ F++TL M +V G+ + ++GG Sbjct: 89 LLA-ASGTPIIFCLLVPIIVGFVVGFFNGAIVTKFKVLSFVTTLAMGTVIGGVTFWLTGG 147 Query: 140 WPI-SPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIGGNMEASK 198 + PE F GQ + +P + M V+ +I + T GRR+YAIGGN +AS+ Sbjct: 148 ATVFENIPEGFKFLGQSKLAFLPTLSVIMFVLVIIFWYIMSQTSLGRRLYAIGGNEKASE 207 Query: 199 LVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVIGGTSLSG 258 + GI R + + + G LAAF G LL + LG A P G G+ L+ AA +G T + Sbjct: 208 VSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTGGDGFFLNAYAAVFLGMTIVKN 267 Query: 259 GEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQI 307 G ILG GA I+G++ NG+ +L V SF Q ++ G +IIIA+ +I Sbjct: 268 GVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIALISQKI 316 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: 288 Number of extensions: 21 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: 313 Length of database: 321 Length adjustment: 27 Effective length of query: 286 Effective length of database: 294 Effective search space: 84084 Effective search space used: 84084 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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