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 GFF3033 PGA1_c30820 putative ABC transporter permease protein
Query= TCDB::G4FGN6 (278 letters) >FitnessBrowser__Phaeo:GFF3033 Length = 320 Score = 127 bits (319), Expect = 3e-34 Identities = 69/223 (30%), Positives = 122/223 (54%), Gaps = 4/223 (1%) Query: 56 NYVKVFKERPFHINIKNSIIVAGITTVLALVVGSLAGYAIARLKFRGKVIVMSLILAVSM 115 NY K F E P + N IIV G ++ +VV A YA+A+LKF G+ V L+L + Sbjct: 101 NYSKAFTEAPLLRYLLNGIIVTGSIFLIQVVVALPAAYALAKLKFWGREAVFGLVLFCLL 160 Query: 116 FPQVSILGSLFLILRGLKLINTYTGLIIPYTAMNLPLTVWVLQSFFRELPKEVEESAFID 175 P +I L+++L L L NTY L++P+T +++++ FF +P ++ ++A +D Sbjct: 161 IPVHAIALPLYIMLAKLGLTNTYAALVVPWTIS--VFGIFLMRQFFMTVPDDLIDAARMD 218 Query: 176 GASKLRTLWSIVLPMSAPGLVATGLLTFIAAWNEFLF-ALTFMQKPSLYTVPVAVALFKG 234 G + +W ++LP + P L+A + + +A WN++ + + L+T P+ + FKG Sbjct: 219 GMGEFSIVWRVMLPTAIPALLAFAIFSIVAHWNDYFWPRIVVTGNRDLFTPPLGLREFKG 278 Query: 235 ASQYEIPWGQLMAAAVIVTLPLVILVLVFQNRIIAGLSAGAVK 277 +G +MA A ++ PL++ L+ Q R I G++ +K Sbjct: 279 DGDGSY-FGPMMATATVIVTPLIVAFLLAQKRFIEGITLSGMK 320 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: 204 Number of extensions: 13 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: 320 Length adjustment: 27 Effective length of query: 251 Effective length of database: 293 Effective search space: 73543 Effective search space used: 73543 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: 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