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_085121058.1 B9O00_RS01465 ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >NCBI__GCF_900177295.1:WP_085121058.1 Length = 335 Score = 225 bits (574), Expect = 1e-63 Identities = 127/309 (41%), Positives = 187/309 (60%), Gaps = 2/309 (0%) Query: 3 KKLFKAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSG 62 K+L + E + + + I L + + FLT NIF ++ I I+S GMT VI+T G Sbjct: 26 KQLATSLELRMLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVILTGG 85 Query: 63 IDLSVGSILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFIST 122 IDLSVGS+ G + +V+GL + + + +++++G+ G G GL +G+LI RLA F+ T Sbjct: 86 IDLSVGSVAGLSGIVLGLALKDYPIP--VAILLGVLTGAGVGLVSGILIGYFRLAAFVVT 143 Query: 123 LGMLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTV 182 LGM+++GR LAY+ SG IS FP + V +P V+++ ++A +L YT Sbjct: 144 LGMMAIGRSLAYIFSGQTAISGFPSDLSSIVYTDVFGIPTNVLFLGFAYLLAWGYLTYTK 203 Query: 183 TGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYE 242 GR IYAIG N EA++ G+ IL Y ++G LAA A A + P G G E Sbjct: 204 GGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDPLTGNGME 263 Query: 243 LDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAI 302 LD IAA VIGG SL GG G+I+G +G +IM ++RNG+ LLGVS FWQ IG +II+A+ Sbjct: 264 LDAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGSIIIMAL 323 Query: 303 AIDQIRRAK 311 ++++ RA+ Sbjct: 324 LVERLVRAR 332 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: 364 Number of extensions: 27 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: 335 Length adjustment: 28 Effective length of query: 285 Effective length of database: 307 Effective search space: 87495 Effective search space used: 87495 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