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 PP_2761 PP_2761 putative Ribose ABC transporter, permease protein
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__Putida:PP_2761 Length = 328 Score = 147 bits (372), Expect = 3e-40 Identities = 94/289 (32%), Positives = 159/289 (55%), Gaps = 9/289 (3%) Query: 16 ILIAIVVFLGVTTREFLTVENIFTVILN-VSFIAIMSFGMTMVIITSGIDLSVGSILGAA 74 + A+++F + FLTV N+ +++LN +AI++ GMT I GIDLSVG+ L + Sbjct: 29 LFAAVLLFFALKAPGFLTVGNLSSLLLNNFVLLAIVAIGMTYAIAAGGIDLSVGTALDFS 88 Query: 75 SVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAY 134 ++ LL++ G ++++ GL G GL N LI R++PF++TLG L +G + Sbjct: 89 ALTFVLLLNA-GFGLYVAIPGGLLAGSLAGLFNAGLIAGLRISPFLATLGTLFIGSSVQK 147 Query: 135 VMS-GGWPISPFPESFTVHG---QGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAI 190 ++S GG PI + E+ G + M+G VP+P++ +A++ ++ + L GR I + Sbjct: 148 LLSEGGQPI--YLEAQVRSGLATERMLG-VPLPLLLVALLALVYGVVLARGRLGREIIVL 204 Query: 191 GGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATV 250 G ++ G+ RI LV+ + F +A AG LL A + P +G + ++ I A Sbjct: 205 GSQPLVARYSGLAQRRIAALVFIASAFASALAGILLPATVNAYAPMSGNAFLMNAIGAVF 264 Query: 251 IGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVII 299 IG T + G LG + + V NG++L+G + FWQQV G++I+ Sbjct: 265 IGATLSLHNRVNVPGTLLGVLFLNVTANGLLLIGWNFFWQQVATGVLIL 313 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: 256 Number of extensions: 22 Number of successful extensions: 4 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: 328 Length adjustment: 28 Effective length of query: 285 Effective length of database: 300 Effective search space: 85500 Effective search space used: 85500 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