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 WP_004115191.1 RHSP_RS09070 carbohydrate ABC transporter permease
Query= TCDB::G4FGN6 (278 letters) >NCBI__GCF_000359745.1:WP_004115191.1 Length = 276 Score = 210 bits (535), Expect = 2e-59 Identities = 107/278 (38%), Positives = 169/278 (60%), Gaps = 2/278 (0%) Query: 1 MSRSITQRILLYIAVVLILIWCVFPLYWAFISSIKPDRDLFEKNPSLFPKRITFENYVKV 60 M RSI I +A++ +++ +FPL+W S+ P+ L+ + ++P R T+E+Y V Sbjct: 1 MRRSIIPTIAHRLAILCYVVFALFPLFWLLKVSVTPNDLLYTEGVRMWPSRTTWEHYSFV 60 Query: 61 FKERPFHINIKNSIIVAGITTVLALVVGSLAGYAIARLKFRGKVIVMSLILAVSMFPQVS 120 + F KNS+IV+ T + + SL+GYA++R FR K +++L+L MFP V Sbjct: 61 LQHSDFPTFFKNSLIVSASTAITVTICASLSGYALSRFTFRAKYWIVALMLLTQMFPLVM 120 Query: 121 ILGSLFLILRGLKLINTYTGLIIPYTAMNLPLTVWVLQSFFRELPKEVEESAFIDGASKL 180 ++ +F IL L L N+ TGL+I YTA N+P +++QSFF +PK++EE+A IDGA++ Sbjct: 121 LVAPIFKILTPLHLTNSLTGLVIVYTAFNVPFATFLMQSFFDGIPKDLEEAAMIDGATQF 180 Query: 181 RTLWSIVLPMSAPGLVATGLLTFIAAWNEFLFALTFMQKPSLYTVPVAVALFKGASQYEI 240 I+LP++ PG+ AT F AAW+E LFAL + T PV + F S++ + Sbjct: 181 TAFRQIILPLTLPGIAATLGFVFTAAWSELLFALMLINGNQAATFPVGLLTF--VSKFSV 238 Query: 241 PWGQLMAAAVIVTLPLVILVLVFQNRIIAGLSAGAVKG 278 +GQ+MAA V+ +P + L+ Q ++ GL+AGAVKG Sbjct: 239 DFGQMMAAGVMALIPAALFFLLIQRYLVQGLTAGAVKG 276 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: 221 Number of extensions: 10 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: 278 Length of database: 276 Length adjustment: 25 Effective length of query: 253 Effective length of database: 251 Effective search space: 63503 Effective search space used: 63503 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 24 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