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_RS32890 RR42_RS32890 ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__Cup4G11:RR42_RS32890 Length = 322 Score = 208 bits (529), Expect = 2e-58 Identities = 115/292 (39%), Positives = 171/292 (58%), Gaps = 1/292 (0%) Query: 20 IVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAASVVMG 79 + + L V + FLT+ NI V+ S + +++ G+T+VI+T G+DLSVG+ + ++ V Sbjct: 27 LCLLLAVASDAFLTLGNILNVLRQASLLFLLASGVTLVILTGGLDLSVGANVAMSACVAA 86 Query: 80 LLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVMSGG 139 +M G S L V GL G GLANGLL+ R+ PFI+T GML V G+ Y G Sbjct: 87 TVMKATG-STMLGVGAGLGTGALIGLANGLLVAMLRIPPFIATYGMLWVLHGVTYWFMAG 145 Query: 140 WPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIGGNMEASKL 199 I FP +F G G + VP+PV M V V + T G+ IYAIG N A++L Sbjct: 146 ETIHGFPPAFRAIGSGYLWGVPIPVYLMLVFLVAGTAMSQKTTYGQEIYAIGANPVAARL 205 Query: 200 VGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVIGGTSLSGG 259 G+ R L+LVY ++G +A A + A L A+ + G+ L IAA +IGGTSL GG Sbjct: 206 SGVPVRRRLVLVYLVSGAMAGIASLVFLARLNSAEGDIGEALTLPAIAAVLIGGTSLFGG 265 Query: 260 EGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIRRAK 311 G + G +GA+I+ ++ NGM LL VS+ WQ +V G+++++A+ +D + R + Sbjct: 266 VGRVSGTLVGAIILTLVLNGMNLLTVSANWQPLVTGVIVVLAVFLDTLSRKR 317 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: 265 Number of extensions: 18 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: 322 Length adjustment: 27 Effective length of query: 286 Effective length of database: 295 Effective search space: 84370 Effective search space used: 84370 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