Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate GFF2854 PS417_14575 MFS transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__WCS417:GFF2854 Length = 445 Score = 207 bits (526), Expect = 9e-58 Identities = 105/314 (33%), Positives = 176/314 (56%), Gaps = 3/314 (0%) Query: 18 KRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFAVRPFGA 77 ++VI A+ +G EW+DF + G LA I++ FF + +AA + T FA FA RP G Sbjct: 15 RKVIIAAGIGNFVEWFDFAVYGFLATTIAQQFFPSGDASAALLKTFAVFAVAFAFRPLGG 74 Query: 78 LVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQGLALGG 137 + FG LGD +GRK T +TI++M +T ++G LP YAAIG+A+P++ +R QG + GG Sbjct: 75 IFFGMLGDRIGRKRTLAMTILLMAGATTLIGLLPTYAAIGVAAPILLSLIRCAQGFSAGG 134 Query: 138 EYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAWGWRIP 197 EY GA Y+ EHAP+++R +Y +++ + + +V + ++ +A G+WGWR+P Sbjct: 135 EYAGACAYLMEHAPSDKRAWYGSFVPVSTFSAFAAAAVVAYALEASLSAEAMGSWGWRLP 194 Query: 198 FVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVILALIGVTA 257 F+ + L + +++R +L E+PAF+ +K E + +PL E +N I L + Sbjct: 195 FLIAAPLGLVGLYLRWKLDETPAFQAVKEEHTVAHSPLKETL---RNHGAAISCLGAFVS 251 Query: 258 GQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIGRKPIIL 317 A+ +Y Y +L + A A ++ IAL+ G SDR+GR+ ++ Sbjct: 252 LTALSFYMFTTYFATYLQVAGGLSRAMALLVSLIALIFAAAICPLAGLYSDRVGRRATVM 311 Query: 318 AGCLIAALTYFPLF 331 C++ + +P F Sbjct: 312 TACVLLMVVVYPSF 325 Score = 50.8 bits (120), Expect = 1e-10 Identities = 31/103 (30%), Positives = 51/103 (49%) Query: 435 LKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSMSLPYH 494 L YP S ++ ++V + +L + + AA+L E FPTR RYT+ ++ Y+ Sbjct: 317 LMVVVYPSFLMASSGSFAASIVGVMLLAVGAVLCGVVTAALLSETFPTRTRYTASAITYN 376 Query: 495 IGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGL 537 + FGG P A +++ G+ S +Y I +AL GL Sbjct: 377 LAYTIFGGTAPLMATWLISTTGSNLSPAFYLIAVALLALAGGL 419 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: 584 Number of extensions: 30 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 552 Length of database: 445 Length adjustment: 34 Effective length of query: 518 Effective length of database: 411 Effective search space: 212898 Effective search space used: 212898 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