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 RR42_RS03365 RR42_RS03365 ribose ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__Cup4G11:RR42_RS03365 Length = 333 Score = 215 bits (548), Expect = 1e-60 Identities = 128/306 (41%), Positives = 180/306 (58%), Gaps = 6/306 (1%) Query: 7 KAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLS 66 + R G+ +L+ + + V T F +N+ + S +++ GMT VI+T GIDLS Sbjct: 25 RLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLS 84 Query: 67 VGSILGAASVVMGL--LMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLG 124 VGSIL ++VV L LM + G+ LSV L G+ FG+ NG L+ +L PFI TLG Sbjct: 85 VGSILSISAVVAMLVSLMPQLGM---LSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLG 141 Query: 125 MLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTG 184 L+ RGLA ++ I F G G V VP VI + ++ L+ TV G Sbjct: 142 TLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLG 201 Query: 185 RRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQP-NAGQGYEL 243 +IYA+GGN EA++L GIK +L+ VY ++G LA G + +A L A GQ YEL Sbjct: 202 LQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYEL 261 Query: 244 DVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIA 303 D IAA ++GGTS GG G+I+G +GA+I+ VL NG++LLGVS WQ ++ G+VII A+A Sbjct: 262 DAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVA 321 Query: 304 IDQIRR 309 +D RR Sbjct: 322 LDSYRR 327 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: 331 Number of extensions: 16 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: 333 Length adjustment: 28 Effective length of query: 285 Effective length of database: 305 Effective search space: 86925 Effective search space used: 86925 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