Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate Pf1N1B4_183 Major facilitator family transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_183 Length = 433 Score = 202 bits (515), Expect = 2e-56 Identities = 114/323 (35%), Positives = 183/323 (56%), Gaps = 13/323 (4%) Query: 14 TKEEKRVIFASSLGTVFEWYDFYLAGSLAAFI-SKSFFSGVNPTAAFIFTLLGFAAGFAV 72 T + +R A+ +GT E+YDFY+ + AA + + FF +P + + FA GF Sbjct: 4 TPQPRRAAAAAFIGTTIEFYDFYIYATAAALVLGQVFFPSHDPVMSTLAAFGSFAVGFIA 63 Query: 73 RPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQG 132 RP +VFG LGD +GRK L+T+ +MGL+T +G LP YA+ G+ +P+ I +RL+QG Sbjct: 64 RPMAGMVFGHLGDRLGRKKMLLVTMALMGLATTGIGMLPSYASAGIWAPIGLIVLRLIQG 123 Query: 133 LALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAW 192 +++GGE+GGA +EHAPA R+ FY ++ Q + GL L+L+ V + ED F AW Sbjct: 124 ISVGGEWGGAVLMASEHAPAKRKTFYASFAQLGSPAGLLLALIAFRLVTSLEPED-FLAW 182 Query: 193 GWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQ-WKNLKIVILA 251 GWR+PF+AS VL+ + + IR +HESP F + K +T+K P+ + W+ ++ A Sbjct: 183 GWRLPFLASGVLMMVGLMIRSGVHESPEFAKAKDNNETAKYPVKDVIRTCWRQ---ILFA 239 Query: 252 LIGVTAGQAVVWYTGQFYALFFLTQTLKVDGAS---ANILIAIALLIGTPFFLFFGSLSD 308 VT G A ++T F + ++TQ + ++ L+ + L+ P L++ Sbjct: 240 AAAVTIGSAGFFFTNTF-MITYVTQYQGIPRSTILDCLFLVTVIQLLSQPLSAL---LAE 295 Query: 309 RIGRKPIILAGCLIAALTYFPLF 331 RIG + L+ +T +P+F Sbjct: 296 RIGEGRFLKLVALLCMVTPYPMF 318 Score = 42.0 bits (97), Expect = 5e-08 Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 4/79 (5%) Query: 450 NWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSMSLPYHIGNGWFGGFLPATAF 509 N + V + + V+ ++ +Y IA + + FP +RY+ +S+ Y + GG P Sbjct: 325 NIVLMTVGIALAVVILSALYAVIAGYMTQAFPVHLRYSGISIAYQLSCALAGGTTPLIG- 383 Query: 510 AIVAAKGNIYSGLWYPIII 528 ++A+K +SG W P+ + Sbjct: 384 TLLASK---FSGQWLPLAV 399 Lambda K H 0.325 0.139 0.422 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: 613 Number of extensions: 36 Number of successful extensions: 6 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: 552 Length of database: 433 Length adjustment: 34 Effective length of query: 518 Effective length of database: 399 Effective search space: 206682 Effective search space used: 206682 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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