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_004129777.1 RHSP_RS32465 ribose ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >NCBI__GCF_000359745.1:WP_004129777.1 Length = 320 Score = 253 bits (646), Expect = 4e-72 Identities = 133/302 (44%), Positives = 187/302 (61%), Gaps = 1/302 (0%) Query: 9 REAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVG 68 R+ I L+ IV F + F+T N ++ S I++ G+T VI+T GIDLSVG Sbjct: 19 RQFSIVLVFFLIVAFFAFANQYFMTWLNWLNLVRQSSINGILAIGVTFVILTKGIDLSVG 78 Query: 69 SILGAASVVMGLLMDEKGLSPFL-SVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLS 127 S++ A ++ L+ E L + GLA G G GL NG+L+ ++ PF+ TLGMLS Sbjct: 79 SVMALAGMIAASLVTETNEQFVLFGIFAGLAAGAGLGLVNGVLVAAVKVPPFVVTLGMLS 138 Query: 128 VGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRI 187 V RGL + S G PI + F G G + +PVP++ + V+ +I L YT GR + Sbjct: 139 VARGLTLIFSEGRPIPNLSDPFKWIGSGQIMYIPVPIVILFVVFLIGWTVLNYTTFGRYV 198 Query: 188 YAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIA 247 YA+GGN +A++ GI T I+ Y I+G LA AG +LTA A P AG GYELD IA Sbjct: 199 YAVGGNEKAARTSGISTKVIVGATYVISGLLAGLAGLVLTARTTAALPQAGIGYELDAIA 258 Query: 248 ATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQI 307 A VIGGTSL+GG G++LG +GA+I+G + NGM L+GVSS++QQV+ G +I++A+ DQI Sbjct: 259 AVVIGGTSLAGGRGSLLGTLIGALIIGTINNGMDLMGVSSYYQQVLKGTIIVVAVIADQI 318 Query: 308 RR 309 R+ Sbjct: 319 RK 320 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: 307 Number of extensions: 15 Number of successful extensions: 2 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: 320 Length adjustment: 27 Effective length of query: 286 Effective length of database: 293 Effective search space: 83798 Effective search space used: 83798 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 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