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 18114 b4086 D-allose transporter subunit (NCBI)
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__Keio:18114 Length = 326 Score = 190 bits (483), Expect = 3e-53 Identities = 110/304 (36%), Positives = 170/304 (55%), Gaps = 2/304 (0%) Query: 5 LFKAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGID 64 LF + F++ I + +F ++ FLT NI + + S ++ G I+ +GID Sbjct: 21 LFWDKYGTFFILAIIVAIFGSLSPEYFLTTNNITQIFVQSSVTVLIGMGEFFAILVAGID 80 Query: 65 LSVGSILGAASVVMGLLMDEKGLSPFLSVVIG-LAVGVGFGLANGLLITKARLAPFISTL 123 LSVG+IL + +V LM G+ PFL+ +IG + VG G NG L+ L PFI TL Sbjct: 81 LSVGAILALSGMVTAKLM-LAGVDPFLAAMIGGVLVGGALGAINGCLVNWTGLHPFIITL 139 Query: 124 GMLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVT 183 G ++ RG+ V+S + F F V +PVPVI+ ++ +I Sbjct: 140 GTNAIFRGITLVISDANSVYGFSFDFVNFFAASVIGIPVPVIFSLIVALILWFLTTRMRL 199 Query: 184 GRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYEL 243 GR IYA+GGN ++ GI +++V+ I+G A AG + TA LG A+P AG G+E Sbjct: 200 GRNIYALGGNKNSAFYSGIDVKFHILVVFIISGVCAGLAGVVSTARLGAAEPLAGMGFET 259 Query: 244 DVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIA 303 IA+ +IGGTS GG+G I +G +I+G + NG+ +L V +++Q VV+G +II A+A Sbjct: 260 YAIASAIIGGTSFFGGKGRIFSVVIGGLIIGTINNGLNILQVQTYYQLVVMGGLIIAAVA 319 Query: 304 IDQI 307 +D++ Sbjct: 320 LDRL 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: 288 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: 326 Length adjustment: 28 Effective length of query: 285 Effective length of database: 298 Effective search space: 84930 Effective search space used: 84930 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 17 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