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_138919826.1 ON01_RS16060 ribose ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >NCBI__GCF_000224785.1:WP_138919826.1 Length = 292 Score = 266 bits (679), Expect = 6e-76 Identities = 138/289 (47%), Positives = 197/289 (68%), Gaps = 3/289 (1%) Query: 20 IVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAASVVMG 79 +V+FLG + F T++NI ++ +S A+++FGMT VI+T+GIDLSVGS+L S + Sbjct: 1 MVIFLGFMSDAFFTLDNILNLLRQISVNALIAFGMTFVILTAGIDLSVGSLLALGSALTA 60 Query: 80 LLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVMSGG 139 L+ G+ P L+V++GL +G+G G NGL+ITK ++APFI+TL ++V RG V + G Sbjct: 61 GLLTS-GMDPMLAVLLGLLIGLGLGAINGLIITKGKVAPFIATLATMTVYRGATLVYTDG 119 Query: 140 WPISPFPESFTVH--GQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIGGNMEAS 197 P++ +SF G G V +P PVI M + +I LK TV GR++YA+GGN E S Sbjct: 120 MPVTGLSDSFAFEMIGGGYVFGIPFPVILMLAVFLILFFVLKKTVFGRQVYAVGGNEEVS 179 Query: 198 KLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVIGGTSLS 257 L GIK DR+ I VY++ G L+ AG +LT+ L AQP AG+ +ELD IAA VIGGTSL Sbjct: 180 VLSGIKADRVKIWVYSLTGMLSVLAGLILTSRLNSAQPTAGEMFELDAIAAVVIGGTSLM 239 Query: 258 GGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQ 306 GG G I G +GA+I+GV+ NG+ L+ VSSF+QQ+V G VI++A+ +D+ Sbjct: 240 GGRGRITGTLIGALIIGVIDNGLNLMNVSSFYQQIVKGGVILLAVLLDR 288 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: 300 Number of extensions: 17 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: 292 Length adjustment: 27 Effective length of query: 286 Effective length of database: 265 Effective search space: 75790 Effective search space used: 75790 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