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_068000560.1 PsAD2_RS00560 ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >NCBI__GCF_001623255.1:WP_068000560.1 Length = 332 Score = 235 bits (599), Expect = 1e-66 Identities = 131/302 (43%), Positives = 180/302 (59%), Gaps = 4/302 (1%) Query: 11 AGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSI 70 AGI L L+A+++F + T FLT NI ++ V+ I++ GMT VI+ GIDLSVGS+ Sbjct: 25 AGIGLALLALILFFSIFTEHFLTANNITNILTQVTINLILAVGMTFVILIGGIDLSVGSV 84 Query: 71 LGAASVVMGLLMDEKGLSPF----LSVVIGLAVGVGFGLANGLLITKARLAPFISTLGML 126 + ASV+ G + GL PF L+V+ AVGV G NG + + L FI TLGML Sbjct: 85 MAFASVIAGKAITLAGLGPFEAIVLAVIAATAVGVVCGAINGTITARWSLPSFIITLGML 144 Query: 127 SVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRR 186 ++ RG A S I FP +F G M VPV + + IA L +TV GR Sbjct: 145 NIARGAALQASNAQTIYSFPLAFEDFGSAMFYGVPVVFMVALALVFIAWFILNFTVFGRL 204 Query: 187 IYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVI 246 +Y IG N EA +L G R I +TI G A A + A L ++ P AG G+EL+ I Sbjct: 205 LYGIGNNEEAVRLAGHSVYRYKIAAFTICGLTAGIAAVVYMARLNISSPIAGIGFELNAI 264 Query: 247 AATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQ 306 AA +IGGTSL+GG G+++G +GA I+GVL NG+IL+G+S F +Q++ G+VIIIA+ +D Sbjct: 265 AAVIIGGTSLNGGRGSVIGTLIGAFIIGVLANGLILIGLSDFMRQMITGVVIIIAVILDY 324 Query: 307 IR 308 R Sbjct: 325 YR 326 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: 303 Number of extensions: 9 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: 332 Length adjustment: 28 Effective length of query: 285 Effective length of database: 304 Effective search space: 86640 Effective search space used: 86640 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