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_RS20745 BPHYT_RS20745 ribose ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__BFirm:BPHYT_RS20745 Length = 341 Score = 209 bits (532), Expect = 7e-59 Identities = 115/303 (37%), Positives = 178/303 (58%), Gaps = 8/303 (2%) Query: 17 LIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAASV 76 LI ++VF + F+ ++N+ ++ + +++ T VIIT GIDLSVG+++ +V Sbjct: 38 LILLLVFFSFASPAFMQMDNMLGILQATAVNGVLAIACTFVIITGGIDLSVGTLMTFTAV 97 Query: 77 VMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVM 136 + G+ + L + V+ + G G +G L K ++ PFI+TLGM+ + +GL+ V+ Sbjct: 98 ICGVFLTYWHLPMWTGVLAAIGTGAICGTVSGTLTAKMKIPPFIATLGMMMLLKGLSLVV 157 Query: 137 SGGWPI--SPFPESFTVHGQGMVG------PVPVPVIYMAVIGVIAHIFLKYTVTGRRIY 188 S PI + + + ++G PVP V+ + + V++ I L T GR + Sbjct: 158 SADKPIYFTDTENFYMISQDSLIGDLLPSLPVPNAVLILFFLAVVSSITLNRTALGRYTF 217 Query: 189 AIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAA 248 A+G N EA +L G+ DR I +Y ++G + AG L+ + L AQP GQGYEL+ IAA Sbjct: 218 ALGSNEEAVRLSGVNVDRWKIAIYGLSGAICGIAGLLIASRLNSAQPALGQGYELEAIAA 277 Query: 249 TVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIR 308 VIGGTSLSGG GTILG +GA IM VL NG+ ++ V+ WQ VV G++II+A+ D +R Sbjct: 278 VVIGGTSLSGGAGTILGTIIGAFIMSVLTNGLRIMSVAQEWQIVVTGLIIILAVYGDILR 337 Query: 309 RAK 311 R K Sbjct: 338 RKK 340 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: 286 Number of extensions: 19 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: 341 Length adjustment: 28 Effective length of query: 285 Effective length of database: 313 Effective search space: 89205 Effective search space used: 89205 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