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 BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__BFirm:BPHYT_RS27190 Length = 343 Score = 232 bits (591), Expect = 1e-65 Identities = 131/311 (42%), Positives = 185/311 (59%), Gaps = 17/311 (5%) Query: 17 LIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAASV 76 L+ ++V +T+ F +V N+ TV L V+ IA + T VIIT GIDLSVGS+L A V Sbjct: 33 LVVLIVAFSLTSAAFFSVGNLMTVALQVTSIAYLGVAATCVIITGGIDLSVGSVLALAGV 92 Query: 77 VMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVM 136 LL+ + G+ ++++ G+ VG G NG+ +T+ L PFI+TLGM+ V RGLA + Sbjct: 93 AAALLV-KAGVPIPVAMLGGMLVGAACGWVNGICVTRMGLPPFIATLGMMLVARGLALQI 151 Query: 137 SGGWPISPFPESFTVHGQGMV----------------GPVPVPVIYMAVIGVIAHIFLKY 180 +G P+S ++F G G + +P PV+ M V+ I L Sbjct: 152 TGARPVSGLGDAFGELGNGALFRISHIGADGFPDTVFPGIPYPVVIMVVLFAAVSILLSR 211 Query: 181 TVTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQG 240 T GR IYA+G N EA++L G+ + + Y ++G LA G +L + L AQPN G Sbjct: 212 TSLGRHIYAVGSNAEAARLSGVNVQGVKLFTYVLSGLLAGATGCVLMSRLVTAQPNEGVM 271 Query: 241 YELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIII 300 YELD IA+ VIGGTSL GG GTI G +GA ++GVLRNG+ + GVSSF QQ++IG+VI+ Sbjct: 272 YELDAIASAVIGGTSLMGGVGTISGTAIGAFVIGVLRNGLNMNGVSSFIQQIIIGVVILG 331 Query: 301 AIAIDQIRRAK 311 + IDQ+R K Sbjct: 332 TVWIDQLRNRK 342 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: 330 Number of extensions: 20 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: 343 Length adjustment: 28 Effective length of query: 285 Effective length of database: 315 Effective search space: 89775 Effective search space used: 89775 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: 49 (23.5 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