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_085635593.1 MGEO_RS05025 ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >NCBI__GCF_002115805.1:WP_085635593.1 Length = 324 Score = 179 bits (454), Expect = 8e-50 Identities = 105/303 (34%), Positives = 171/303 (56%), Gaps = 6/303 (1%) Query: 6 FKAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDL 65 F AR+ GI + +V + + F+ +NI VI + + + +M+ G+T V+I+ +DL Sbjct: 12 FLARQ-GILVAFAVFMVGFTLANQRFVDPDNILGVIRSSAILGVMALGVTFVVISGNLDL 70 Query: 66 SVGSILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGM 125 SVGS++ +++V+ L D+ G P L++ A+ + G G L+ +L I TLGM Sbjct: 71 SVGSMMSFSTIVVLDLHDKIG--PALAIPAMFAMTLCLGAFIGFLVGYLKLNSLIVTLGM 128 Query: 126 LSVGRGLAYVMSGGWPISPFPES---FTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTV 182 LS GL SGG + + F GQG +PVP++ ++ + + L T Sbjct: 129 LSAIHGLTLTYSGGQNMDIADKEGTWFDFFGQGSALGIPVPILIFVLLAAVLGVVLSKTP 188 Query: 183 TGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYE 242 GR++YA+GGN A+ GI+ R++ Y I+ F A AG L + +Q GQG E Sbjct: 189 FGRKVYAVGGNGTAATFSGIRRARVVFTCYLISAFCVATAGLLQASRSLGSQNTVGQGLE 248 Query: 243 LDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAI 302 L+V+AA ++GG SL GG GTI +G +I+G ++NG++L+G+ + Q VV I+II+A+ Sbjct: 249 LEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLQFYVQYVVTWIIIILAV 308 Query: 303 AID 305 +D Sbjct: 309 WLD 311 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: 337 Number of extensions: 22 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