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 3606962 Dshi_0389 Monosaccharide-transporting ATPase (RefSeq)
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__Dino:3606962 Length = 357 Score = 187 bits (476), Expect = 2e-52 Identities = 109/302 (36%), Positives = 173/302 (57%), Gaps = 8/302 (2%) Query: 13 IFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILG 72 + +++ AI VF + +F + + ++ V + I++ ++VI+T+GIDLSVG+I+ Sbjct: 49 LIVLVAAIAVFGLLLGSKFFSPFALTLILQQVQIVGIVAAAQSLVILTAGIDLSVGAIMV 108 Query: 73 AASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGL 132 +SVVMG GL ++V GL G G NG L+ K +L PFI TLGM + Sbjct: 109 MSSVVMGQFTFRYGLPVEVAVACGLLCGTLLGFINGWLVAKVKLPPFIVTLGMWQIVLAA 168 Query: 133 AYVMSGGWPI--------SPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTG 184 ++ S I +P + F + + VI+M ++ ++ L++T G Sbjct: 169 NFLYSRNETIRSQDIRDQAPLLQFFGTTLEIGGARLTYGVIFMVLLVIVLAYALRHTAWG 228 Query: 185 RRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELD 244 R +YA+G + EA++L G++ R LI VY ++G + AFAG+ L +G P +GQ ++ Sbjct: 229 RHVYAVGDDPEAAELSGVQVSRTLISVYMLSGLICAFAGWALIGRIGSVSPTSGQLANIE 288 Query: 245 VIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAI 304 I A VIGG SL GG G+ILGAF GA+I+GV G+ LLG + W ++IG++II A+A+ Sbjct: 289 SITAVVIGGISLFGGRGSILGAFFGALIVGVFTLGLRLLGADAQWTFLLIGLLIIAAVAV 348 Query: 305 DQ 306 DQ Sbjct: 349 DQ 350 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: 284 Number of extensions: 12 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: 357 Length adjustment: 28 Effective length of query: 285 Effective length of database: 329 Effective search space: 93765 Effective search space used: 93765 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: 49 (23.5 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