Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate GFF2070 PS417_10555 major facilitator transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__WCS417:GFF2070 Length = 541 Score = 674 bits (1739), Expect = 0.0 Identities = 320/541 (59%), Positives = 416/541 (76%), Gaps = 14/541 (2%) Query: 8 ISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFA 67 ++ A E K+VIFASSLGTVFEWYDF+L G+LAA ISK FF+GVN T AFIF L+ FA Sbjct: 12 VNTAITRNESKKVIFASSLGTVFEWYDFFLYGALAAVISKQFFAGVNDTTAFIFALMAFA 71 Query: 68 AGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAM 127 AGF VRPFGALVFGRLGDM+GRKYTFL+TI++MG++T VG LP YA+IG+A+P+I I + Sbjct: 72 AGFVVRPFGALVFGRLGDMIGRKYTFLVTIILMGVATFCVGLLPTYASIGIAAPIILIVL 131 Query: 128 RLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGED 187 R+LQGLALGGEYGGAATYVAEHAPA +RGF+T+WIQ+TATLGL LSLLV+L R G D Sbjct: 132 RMLQGLALGGEYGGAATYVAEHAPAGKRGFHTSWIQSTATLGLLLSLLVVLACRYFTG-D 190 Query: 188 AFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKI 247 F WGWRIPF+ S+VLLGIS WIRM LHESPAF ++K EGK SK+P+ ++FG+W+NLKI Sbjct: 191 QFEVWGWRIPFLFSIVLLGISTWIRMSLHESPAFLKMKEEGKASKSPIRDSFGKWENLKI 250 Query: 248 VILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLS 307 V++AL + GQAV +Y QFY LFFLTQ LK+D A AN+L+ I+++IG PFF+FFG LS Sbjct: 251 VLIALFSINGGQAVTFYAAQFYVLFFLTQFLKMDPALANMLLIISVVIGAPFFIFFGWLS 310 Query: 308 DRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQFNPV 367 D++GRKP+++ G L+A YFP+FK+L HY NPA++ A+ ++PI V+A+P C+FQF+PV Sbjct: 311 DKVGRKPVLMLGLLLATALYFPIFKSLAHYTNPAMDQASNQAPITVLADPATCTFQFDPV 370 Query: 368 GTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADAKDAGKAF 427 G +KF S CD K+ L K GL Y + AAPAG+ Q+ VGD I+ +D KA Sbjct: 371 GKAKFDSPCDKVKTFLVKQGLPYSSAAAPAGSPVQVSVGDVRIEGFDEKA---------- 420 Query: 428 DKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYT 487 L A+ A YP AD +Q+N M VV++ L++ M YGP+AA++VE+FPTRIRYT Sbjct: 421 ---LRGAVTLAGYPSSADVAQVNKTMVVVLIVALILIAAMCYGPLAALMVELFPTRIRYT 477 Query: 488 SMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVRETKDSN 547 SMSLPYHIGNGWFGGFLP +FA+V G+I+ GLWYP+++ + ++G++ ++ET+ + Sbjct: 478 SMSLPYHIGNGWFGGFLPTVSFALVVYTGDIFYGLWYPVVVTGVSLIVGMICLKETRHVD 537 Query: 548 I 548 I Sbjct: 538 I 538 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: 833 Number of extensions: 36 Number of successful extensions: 7 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: 541 Length adjustment: 36 Effective length of query: 516 Effective length of database: 505 Effective search space: 260580 Effective search space used: 260580 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