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 Pf1N1B4_692 ABC spermidine/putrescine transporter, inner membrane subunit
Query= TCDB::G4FGN6 (278 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_692 Length = 282 Score = 85.9 bits (211), Expect = 9e-22 Identities = 51/155 (32%), Positives = 85/155 (54%), Gaps = 1/155 (0%) Query: 73 SIIVAGITTVLALVVGSLAGYAIARLKFRGKVIVMSLILAVSMFPQVSILGSLFLILRGL 132 S++VA +T + A ++ A YA+ R +FRGK + + L+ +FP V + +L L+ L Sbjct: 86 SLMVACLTMIFATIIAVPAAYALTRCEFRGKAVALQLMSLPLVFPMVVLGLALLLVFDSL 145 Query: 133 KLINTYTGLIIPYTAMNLPLTVWVLQSFFRELPKEVEESAFIDGASKLRTLWSIVLPMSA 192 T + L+I + + LP V + + EVEE+A + GAS LR + +V+P+ Sbjct: 146 PFHITTSRLVIAHVILALPFVVKNCTAAMLSIGSEVEEAAQMLGASPLRAIVDVVVPLMK 205 Query: 193 PGLVATGLLTFIAAWNEFLFALTFMQKPSLYTVPV 227 G++A LL FI ++NEF F+ + TVP+ Sbjct: 206 SGILAGMLLAFIVSFNEFTVTY-FLYTIDVMTVPI 239 Score = 23.5 bits (49), Expect = 0.006 Identities = 28/149 (18%), Positives = 54/149 (36%), Gaps = 10/149 (6%) Query: 45 PSLFPKRITFENYVKVFKERPFHINIKNSIIVAGITTVLALVVG-------SLAGYAIAR 97 P +FP + + VF PFHI + +++A + L VV S+ Sbjct: 126 PLVFPMVVLGLALLLVFDSLPFHIT-TSRLVIAHVILALPFVVKNCTAAMLSIGSEVEEA 184 Query: 98 LKFRGKVIVMSLILAVSMFPQVSILGSLFLILRGLKLINTYTGLIIPYTAMNLPLTVWVL 157 + G + +++ V + IL + L + N +T YT + + +W+ Sbjct: 185 AQMLGASPLRAIVDVVVPLMKSGILAGMLLAF--IVSFNEFTVTYFLYTIDVMTVPIWMY 242 Query: 158 QSFFRELPKEVEESAFIDGASKLRTLWSI 186 L V A + +W++ Sbjct: 243 SRTVSSLDPTVFSFAVLIVLIDFVLIWAL 271 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: 182 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 278 Length of database: 282 Length adjustment: 26 Effective length of query: 252 Effective length of database: 256 Effective search space: 64512 Effective search space used: 64512 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