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 AZOBR_RS31200 AZOBR_RS31200 sugar ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__azobra:AZOBR_RS31200 Length = 325 Score = 171 bits (432), Expect = 3e-47 Identities = 92/282 (32%), Positives = 162/282 (57%), Gaps = 7/282 (2%) Query: 31 FLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAASVVMGLLMDEKGLSPF 90 F ++ + ++ + +F+ I + GMT VI++ GIDLSVG+++G +V++ +L+++ G P Sbjct: 29 FASLRVVGNLLTDNAFLGITAVGMTFVILSGGIDLSVGAVIGFTTVLLAVLIEQGGWHPV 88 Query: 91 LSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVMSG-----GWPISPF 145 + + LAV GFG A G +I ++ PFI TL + V RGL +V+S P+ Sbjct: 89 SAFAVALAVAGGFGAAMGAVIHVFQMPPFIVTLAGMFVARGLGFVLSTDSIPINHPLYAE 148 Query: 146 PESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIGGNMEASKLVGIKTD 205 + G G + +P + M + A + +T G +YA+GGN ++++L+G+ Sbjct: 149 LGDLALRFDGG-GKLTLPALLMLGVVAAAVVCAHWTRFGANLYALGGNRQSAELMGVPVG 207 Query: 206 RILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVIGGTSLSGGEGTILG 265 R + VY ++G LA AG + + + G A G ELD I A VIGGT L+GG G ++G Sbjct: 208 RTTVAVYALSGLLAGLAGIVFSLYTGAGYSLAATGVELDTITAVVIGGTQLTGGYGYVIG 267 Query: 266 AFLGAVIMGVLRNGMILLG-VSSFWQQVVIGIVIIIAIAIDQ 306 F+G +I G+++ + G +SS+W ++ IG+++ + I + + Sbjct: 268 TFIGVLIQGLIQTYITFDGSLSSWWTKIAIGVLLFVFILLQK 309 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: 327 Number of extensions: 22 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: 325 Length adjustment: 28 Effective length of query: 285 Effective length of database: 297 Effective search space: 84645 Effective search space used: 84645 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