Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate BWI76_RS21415 BWI76_RS21415 MFS transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__Koxy:BWI76_RS21415 Length = 432 Score = 206 bits (523), Expect = 2e-57 Identities = 114/328 (34%), Positives = 183/328 (55%), Gaps = 9/328 (2%) Query: 14 TKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFAVR 73 T+ I +S G + EW+DFY+ + + + FF N T + T FAAGF +R Sbjct: 17 TRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFAAGFLMR 76 Query: 74 PFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQGL 133 P G +FGR+ D GRK + LI++ +M + V+ LPGYA IG +P + + RL QGL Sbjct: 77 PIGGWIFGRIADRRGRKTSMLISVCMMCFGSLVIACLPGYATIGTWAPALLLLARLFQGL 136 Query: 134 ALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAWG 193 ++GGEYG +ATY++E A ++GFY ++ T G L++LV++ ++ + ++A AWG Sbjct: 137 SVGGEYGTSATYMSEVAVEGKKGFYASFQYVTLIGGQLLAVLVVVALQQILSDEALHAWG 196 Query: 194 WRIPFVASLVLLGISVWIRMQLHESPAFE-RIKAEGKTSKAPLSEAFGQWKNLKIVILAL 252 WRIPF VL +++W+R QL E+ E R E + K G W+N K I+ L Sbjct: 197 WRIPFALGAVLAIVALWLRRQLDETSKQETRALKEAGSFK-------GLWRNRKAFIMVL 249 Query: 253 IGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIGR 312 G TA ++ +YT Y +L T + +A++++ AL + FG+LSD+IGR Sbjct: 250 -GFTAAGSLSFYTFTTYMQKYLVNTAGMTAGTASMIMTAALFVYMLVQPLFGALSDKIGR 308 Query: 313 KPIILAGCLIAALTYFPLFKALTHYANP 340 + +L ++ + P+ AL + ++P Sbjct: 309 RTSMLCFGVLVTVFTVPILNALQNVSSP 336 Score = 45.1 bits (105), Expect = 6e-09 Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 2/94 (2%) Query: 452 PMTVVILTILVIYVTMVYGPIAAML-VEMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFA 510 P L I + + Y I+ +L EMFP ++R + L Y + N FGG A + Sbjct: 336 PYAAFALVICALLIVSFYTSISGILKAEMFPAQVRALGVGLSYAVANALFGGSAEYVALS 395 Query: 511 IVAAKGNIYSGLWYPIIIALATFVIGLLFVRETK 544 + +A G ++ WY ++ F++ L R+ K Sbjct: 396 LKSA-GIEHAFYWYVTVMGAIAFLVSLTLHRKGK 428 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: 562 Number of extensions: 29 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: 432 Length adjustment: 34 Effective length of query: 518 Effective length of database: 398 Effective search space: 206164 Effective search space used: 206164 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