Align ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized)
to candidate RR42_RS22885 RR42_RS22885 sugar ABC transporter permease
Query= TCDB::G4FGN6 (278 letters) >FitnessBrowser__Cup4G11:RR42_RS22885 Length = 288 Score = 151 bits (381), Expect = 2e-41 Identities = 83/272 (30%), Positives = 151/272 (55%), Gaps = 10/272 (3%) Query: 12 YIAVVLILI-WCVFPLYWAFISSIKPDRDLFE--KNPSLFPKRITFENYVKVFKERPFHI 68 ++A++ + +C FP YW I++ K DL NP LF + T +N +F E + Sbjct: 21 HVAILAVFAGFCAFPFYWMLITTFKDVHDLINTANNPFLFNQPPTLDNLRVLFLETQYLR 80 Query: 69 NIKNSIIVAGITTVLALVVGSLAGYAIARLK-FRGKVIVMSLILAVSMFPQVSILGSLFL 127 I N+++V + + L++ AGY++ARL RG+ + +++ L + P + + Sbjct: 81 WIANTLLVGAMVVAITLLLAVPAGYSLARLAGSRGRQLAIAIFLTYLIPPTILFI-PFSR 139 Query: 128 ILRGLKLINTYTGLIIPYTAMNLPLTVWVLQSFFRELPKEVEESAFIDGASKLRTLWSIV 187 I+ L L ++ L++ Y + +P W++ FF+ +P+++EE+A +DG S+ +V Sbjct: 140 IIGALGLQDSLWSLVLVYPSFTVPFCTWLMMGFFKAVPRDIEEAAMMDGLSRFGAFLKVV 199 Query: 188 LPMSAPGLVATGLLTFIAAWNEFLFALTFMQKPSLYTVPVAVALF--KGASQYEIPWGQL 245 +P+S+ G++ + T EF++ALTF+ S YTV V V F +G + WG L Sbjct: 200 VPLSSAGILTVVIFTLTLVMQEFVYALTFITSSSQYTVSVGVPTFLVRGDVYF---WGSL 256 Query: 246 MAAAVIVTLPLVILVLVFQNRIIAGLSAGAVK 277 M A ++V++P+ +L +F +R +AG + GAVK Sbjct: 257 MGACLVVSVPVAVLYNLFVDRFVAGFTVGAVK 288 Lambda K H 0.329 0.142 0.424 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: 213 Number of extensions: 11 Number of successful extensions: 4 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: 278 Length of database: 288 Length adjustment: 26 Effective length of query: 252 Effective length of database: 262 Effective search space: 66024 Effective search space used: 66024 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 (21.8 bits) S2: 47 (22.7 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