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 3608247 Dshi_1651 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::G4FGN7 (293 letters) >FitnessBrowser__Dino:3608247 Length = 334 Score = 128 bits (321), Expect = 2e-34 Identities = 91/291 (31%), Positives = 154/291 (52%), Gaps = 20/291 (6%) Query: 11 WMIL-PTILVISVVAFFPLFKTFYDSFYSFGLRPGIERRFVGLQNYFRLFEDTRFIMALK 69 W+ L P + V+ + +P+ +T S PG ++VGL NY ++ + +F A++ Sbjct: 54 WIFLFPALFVLLLYLGYPVVETLRLSLLE--RVPGGGYQWVGLDNYAQMASEPKFWEAMR 111 Query: 70 NTVFFTVISVSLETVLGVLIAIVVHQRFALRGVVRAAMLVPWAIPTAISSQMWRWMF--- 126 N +F+ ++ +L T G+L A + R V ++ + +P AI +S +W+ ++ Sbjct: 112 NNMFWLIVVPALSTAFGLLAAQLT-DRIKWGNVAKSIIFMPMAISFVGASVIWKLVYDGR 170 Query: 127 ---HDQFGIMSRLWEKLGIIEPGTPI--LGTPGLAMWAIIFVDVWKTTPFMALLILAGLQ 181 +Q GI++ + LG G P+ L P + ++ V VW T F +++ A L+ Sbjct: 171 PIEQEQIGILNAIIVGLG----GDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALR 226 Query: 182 VIPEDIYEAARIDGANTIQRFFRITLPLITPTIGVALIFRTLDALRVFDVVYIMTRGAVN 241 IPE+ EAA IDGA+ +Q FF+I +P I PT+ V TL L+VFD+V+ MT G Sbjct: 227 GIPEETIEAAIIDGASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNGQWE 286 Query: 242 TETLAVYNRHVLMDRAFTGAWFGYGSAISVFIFVLISVFAILYIKSLRLKL 292 T+ LA Y + D+ F +G GSA ++ I +L++ I I S R ++ Sbjct: 287 TQVLANY----MFDKLFRANDWGVGSASAMVIMLLVTPILIWNIHSARKEM 333 Lambda K H 0.333 0.145 0.457 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: 310 Number of extensions: 20 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: 293 Length of database: 334 Length adjustment: 27 Effective length of query: 266 Effective length of database: 307 Effective search space: 81662 Effective search space used: 81662 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (21.5 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