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_110753066.1 C7477_RS13715 carbohydrate ABC transporter permease
Query= TCDB::G4FGN6 (278 letters) >NCBI__GCF_003217235.1:WP_110753066.1 Length = 274 Score = 179 bits (454), Expect = 6e-50 Identities = 101/276 (36%), Positives = 163/276 (59%), Gaps = 6/276 (2%) Query: 3 RSITQRILLYIAVVLILIWCVFPLYWAFISSIKPDRDLFEKNPSLFPKRITFENYVKVFK 62 +SI ++ + V +I+ +F W S+K + D P L P+R + NY ++F Sbjct: 4 KSILSKLGTALLVFVIVSPAIFFFVWMLSLSLKYEIDNGAYPPILIPERFAWSNYTQIFA 63 Query: 63 ERPFHINIKNSIIVAGITTVLALVVGSLAGYAIARLKFRGKVIVMSLILAVSMFPQVSIL 122 E F + NS++V G+ T+LAL+VG AGY IARLK +V I+ M P +S L Sbjct: 64 ENDFLLYFWNSLLVTGMATLLALLVGVPAGYGIARLKAHKSAVV---IMIARMTPGLSYL 120 Query: 123 GSLFLILRGLKLINTYTGLIIPYTAMNLPLTVWVLQSFFRELPKEVEESAFIDGASKLRT 182 LFL+ + L L+ T II + + +P+ +W++ +F P E+EE+A IDGA+ + Sbjct: 121 IPLFLLFQTLGLLGTLWPQIIIHLVVTVPIVIWIMIGYFEATPMELEEAAQIDGANAWQV 180 Query: 183 LWSIVLPMSAPGLVATGLLTFIAAWNEFLFALTFMQKPSLYTVPVAVALFKGASQYEIPW 242 + LP++ PG+V + +L I +WN F+F + + + T+PVAV + S ++ W Sbjct: 181 FRLVALPIAKPGIVVSLILAVIFSWNNFVFGIVLASRET-RTLPVAV--YNMLSFEQVSW 237 Query: 243 GQLMAAAVIVTLPLVILVLVFQNRIIAGLSAGAVKG 278 G L AAA++VTLP+++L ++ Q +I+AGL+AGAVKG Sbjct: 238 GPLAAAALVVTLPVLLLTVLAQRQIVAGLTAGAVKG 273 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: 12 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: 278 Length of database: 274 Length adjustment: 25 Effective length of query: 253 Effective length of database: 249 Effective search space: 62997 Effective search space used: 62997 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