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 Synpcc7942_0948 Synpcc7942_0948 permease protein of sugar ABC transporter
Query= TCDB::G4FGN6 (278 letters) >FitnessBrowser__SynE:Synpcc7942_0948 Length = 275 Score = 223 bits (567), Expect = 5e-63 Identities = 112/267 (41%), Positives = 180/267 (67%), Gaps = 1/267 (0%) Query: 13 IAVVLILIWCVFPLYWAFISSIKPDRDLFEKNPSLFPKRITFENYVKVFKERP-FHINIK 71 IA + + ++ + P+ W ++SIK + D+ +P++ T E+Y ++++ P F + Sbjct: 9 IAALALSLFSLAPILWQLLTSIKVNADIAAIPTIYWPRQWTVEHYQALWQQTPAFGRYLL 68 Query: 72 NSIIVAGITTVLALVVGSLAGYAIARLKFRGKVIVMSLILAVSMFPQVSILGSLFLILRG 131 NS +V+ I T+ AL++G+ YAIAR + R +++ +L V++FP V + L ++R Sbjct: 69 NSAVVSAIATLAALLIGTPCAYAIARRRDRSSQVLVGSLLLVTLFPYVLLFQGLLEVVRW 128 Query: 132 LKLINTYTGLIIPYTAMNLPLTVWVLQSFFRELPKEVEESAFIDGASKLRTLWSIVLPMS 191 L+ N Y L++PYTA+NLPL + +L+SFF +LP E+EE+A IDG S + LW I++P++ Sbjct: 129 LQWGNNYAALVVPYTALNLPLVILLLRSFFEQLPPELEEAAQIDGLSLGQRLWLILVPLT 188 Query: 192 APGLVATGLLTFIAAWNEFLFALTFMQKPSLYTVPVAVALFKGASQYEIPWGQLMAAAVI 251 AP LV G+L FI +WNE++ AL+F+ + +L TVP+AVA G S +++P+G + AA V+ Sbjct: 189 APALVTAGILAFIFSWNEYVLALSFISQQALKTVPIAVAEIGGISIFDVPYGDIAAATVV 248 Query: 252 VTLPLVILVLVFQNRIIAGLSAGAVKG 278 TLPL+ LVLV Q RI+ GL+AGAVKG Sbjct: 249 ATLPLIGLVLVAQRRILEGLTAGAVKG 275 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: 228 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: 275 Length adjustment: 25 Effective length of query: 253 Effective length of database: 250 Effective search space: 63250 Effective search space used: 63250 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