Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate Pf6N2E2_2095 Permeases of the major facilitator superfamily
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2095 Length = 540 Score = 675 bits (1742), Expect = 0.0 Identities = 319/535 (59%), Positives = 415/535 (77%), Gaps = 14/535 (2%) Query: 14 TKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFAVR 73 ++E ++VIFASSLGTVFEWYDF+L G+LAA ISK FF+GVN T AFIF L+ FAAGF VR Sbjct: 17 SQETQKVIFASSLGTVFEWYDFFLYGALAAVISKQFFAGVNDTTAFIFALMAFAAGFIVR 76 Query: 74 PFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQGL 133 PFGALVFGRLGDM+GRKYTFL TI++MG++T VG LP YA+IG+A+P+I + +R+LQGL Sbjct: 77 PFGALVFGRLGDMIGRKYTFLATIILMGVATFCVGLLPNYASIGIAAPIILVVLRMLQGL 136 Query: 134 ALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAWG 193 ALGGEYGGAATYVAEHAP +RGF+T+WIQ+TATLGL LSLLV+LG R G D F WG Sbjct: 137 ALGGEYGGAATYVAEHAPMGKRGFHTSWIQSTATLGLLLSLLVVLGCRYFTG-DQFEVWG 195 Query: 194 WRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVILALI 253 WRIPF+ S++LLGIS WIR+ LHESPAF ++K EGK+ KAP+ E+FG+W+NLK+V++AL Sbjct: 196 WRIPFLLSILLLGISTWIRLSLHESPAFLKMKEEGKSCKAPIRESFGKWENLKVVLIALF 255 Query: 254 GVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIGRK 313 + AGQAV +Y QFY LFFLTQ LK+D A AN L+ ++++IG PFF+FFG LSD++GRK Sbjct: 256 SINAGQAVTFYAAQFYVLFFLTQFLKMDPALANSLLIVSVVIGAPFFIFFGWLSDKVGRK 315 Query: 314 PIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQFNPVGTSKFT 373 P+++ G L+A YFP+FK L HYANPA++ A++++PI VIA+P C+FQF+PVG ++F Sbjct: 316 PVLMIGLLLATALYFPIFKTLAHYANPAIDQASRQAPITVIADPATCTFQFDPVGKARFD 375 Query: 374 SSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADAKDAGKAFDKNLGT 433 S CD K+ L K GL Y +VAAPAG+ Q+ VGD ++ YD A L Sbjct: 376 SPCDKVKTFLVKQGLPYSSVAAPAGSTVQVSVGDVKLEGYDEAA-------------LRG 422 Query: 434 ALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSMSLPY 493 A+ A YP +AD Q+N PM V ++ L+I M YGP+AA++VE+FPTRIRYTSMSLPY Sbjct: 423 AVTLAGYPQQADAQQINRPMIVALIVALIIISAMCYGPLAALMVELFPTRIRYTSMSLPY 482 Query: 494 HIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVRETKDSNI 548 HIGNGWFGGFLP +FA+V G+I+ GLWYP++I + V+G++ +RET+ ++ Sbjct: 483 HIGNGWFGGFLPTVSFALVVYTGDIFYGLWYPVVITGVSLVVGMICLRETRSVDL 537 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: 845 Number of extensions: 41 Number of successful extensions: 8 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: 552 Length of database: 540 Length adjustment: 35 Effective length of query: 517 Effective length of database: 505 Effective search space: 261085 Effective search space used: 261085 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