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 CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 233 bits (595), Expect = 4e-66 Identities = 124/306 (40%), Positives = 189/306 (61%), Gaps = 4/306 (1%) Query: 8 AREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSV 67 AR+ L L+ +V G FLT N ++ VS I++ GMT VI+ GID++V Sbjct: 23 ARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAV 82 Query: 68 GSILGAASV----VMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTL 123 GS+L AS+ V+ ++ + + +++++ +G+ G G +T + FI TL Sbjct: 83 GSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTL 142 Query: 124 GMLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVT 183 G ++V RG +++ G PIS F +++ G G + +PVPV+ A++ H+ L+YT Sbjct: 143 GGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRY 202 Query: 184 GRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYEL 243 GR++YA+GGN EA++L G+ D I VY I G LA +GFLL+A LG A+ AG GYEL Sbjct: 203 GRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYEL 262 Query: 244 DVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIA 303 VIA+ VIGG SL+GG G + G LGA+++GVL NG+++L V+S+ QQVVIG++I+ A+A Sbjct: 263 RVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVA 322 Query: 304 IDQIRR 309 D R Sbjct: 323 FDHYAR 328 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: 306 Number of extensions: 21 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: 332 Length adjustment: 28 Effective length of query: 285 Effective length of database: 304 Effective search space: 86640 Effective search space used: 86640 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