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_004129723.1 RHSP_RS32355 hypothetical protein
Query= TCDB::G4FGN4 (313 letters) >NCBI__GCF_000359745.1:WP_004129723.1 Length = 324 Score = 249 bits (637), Expect = 5e-71 Identities = 140/303 (46%), Positives = 192/303 (63%), Gaps = 2/303 (0%) Query: 11 AGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSI 70 AG++L + ++V LG F T N+ V+ IA+++FG T VI GIDLSVGS Sbjct: 22 AGVYLAFVVLLVALGFAAPRFFTFGNLTDVLRQAVPIAVIAFGTTFVIGMRGIDLSVGST 81 Query: 71 LGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGR 130 L + +V L+ G L+ G+AVG GL NG+LITK + FI+T+ ++ + R Sbjct: 82 LALSGLVTANLI-VLGYPVPLACAGGIAVGAVIGLVNGILITKVGITDFIATMAIMVISR 140 Query: 131 GLAYVMSGGWPISPFPE-SFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYA 189 G+ V + G PI + +F + GQ G VPVPVI A++ IA L YT GR + + Sbjct: 141 GIVMVYTQGIPIVGASDPAFRMIGQSYAGGVPVPVILTAIVFAIAFYLLYYTRFGRFVLS 200 Query: 190 IGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAAT 249 IG N +A++LVGI TD++ I VY + G L+AFAG LLT+ L A P AGQGYELDVIAA Sbjct: 201 IGSNPDAARLVGIPTDKVKIAVYVLVGVLSAFAGVLLTSRLEAAMPEAGQGYELDVIAAV 260 Query: 250 VIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIRR 309 VIGGT LSGG T+ G +GAV+M V+RN + LL V++FW QVVIG +I+IA+A D+ R Sbjct: 261 VIGGTGLSGGRATLFGTAVGAVLMAVVRNALNLLNVNTFWHQVVIGTIILIAVAADRFSR 320 Query: 310 AKE 312 ++ Sbjct: 321 RQK 323 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: 329 Number of extensions: 15 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: 324 Length adjustment: 27 Effective length of query: 286 Effective length of database: 297 Effective search space: 84942 Effective search space used: 84942 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