Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate WP_057507085.1 ABB28_RS02395 MFS transporter
Query= TCDB::F8SVK1 (552 letters) >NCBI__GCF_001431535.1:WP_057507085.1 Length = 549 Score = 714 bits (1842), Expect = 0.0 Identities = 359/542 (66%), Positives = 431/542 (79%), Gaps = 6/542 (1%) Query: 11 APMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGF 70 A +TK K+VIFASSLGTVFEWYDF+L GSLAA I+K FFSGVN T IF LL FAAGF Sbjct: 8 AQLTKGHKKVIFASSLGTVFEWYDFFLYGSLAAIIAKQFFSGVNETTGMIFALLAFAAGF 67 Query: 71 AVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLL 130 VRPFGA FG LGD +GRKYTFL+TI+IMG+ST +VG LP YA+IG A+PVI I +RL Sbjct: 68 FVRPFGAAFFGSLGDRIGRKYTFLVTILIMGISTFLVGVLPNYASIGFAAPVILIILRLA 127 Query: 131 QGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFG 190 QGLA+GGEYGGAATYVAEHAPAN+RG YT++IQ TATLGLF+SLL+IL R +G +AF Sbjct: 128 QGLAMGGEYGGAATYVAEHAPANKRGLYTSFIQCTATLGLFMSLLIILACRYFLGNEAFE 187 Query: 191 AWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVIL 250 AWGWRIPF+ S+VLLGISVWIR+QL ESP F+++KAEGK SK P ++ NLK+++L Sbjct: 188 AWGWRIPFLVSIVLLGISVWIRLQLSESPLFQQMKAEGKGSKTPFRDSLKD-GNLKLMLL 246 Query: 251 ALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRI 310 L+G AGQAVVWY GQFYALFFL+ LKVD ++ +LIA AL +G PFF+FFG LSDRI Sbjct: 247 VLLGAAAGQAVVWYGGQFYALFFLSSMLKVDATTSYLLIAAALALGVPFFIFFGWLSDRI 306 Query: 311 GRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQFNPVGTS 370 GRK IILAGCL+AA+TY P+FK LTH+ANPA+E A SP +VIA+P+ CSFQF+PVG Sbjct: 307 GRKWIILAGCLLAAVTYIPVFKGLTHFANPAIEEARSSSPALVIADPNTCSFQFDPVGLR 366 Query: 371 KFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADAKDAGKAFDKN 430 KFTSSCD+A +AL+KAG+ YD APAG+LA + VG + + +Y+ A AK+ GKA Sbjct: 367 KFTSSCDVATAALTKAGVPYDVQPAPAGSLAVVNVGTSKVSSYEA-AGLAKEDGKAKADA 425 Query: 431 LGTALKA----ASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRY 486 GT LKA A YP KAD +++N P T+ +L ILV+YVTMVYGPIAA LVE+FPTRIRY Sbjct: 426 FGTELKAALVEAGYPAKADNARINIPGTIFMLWILVLYVTMVYGPIAAYLVELFPTRIRY 485 Query: 487 TSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVRETKDS 546 TSMSLPYHIGNGWFGGFLPA +FA+VA GN+Y GLWYPI IAL T VIG LF+ +TK+ Sbjct: 486 TSMSLPYHIGNGWFGGFLPAISFALVAGTGNLYYGLWYPIAIALMTVVIGGLFLHDTKNV 545 Query: 547 NI 548 +I Sbjct: 546 DI 547 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: 892 Number of extensions: 36 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: 549 Length adjustment: 36 Effective length of query: 516 Effective length of database: 513 Effective search space: 264708 Effective search space used: 264708 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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