Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate WP_012384331.1 BIND_RS06770 MFS transporter
Query= TCDB::F8SVK1 (552 letters) >NCBI__GCF_000019845.1:WP_012384331.1 Length = 568 Score = 694 bits (1790), Expect = 0.0 Identities = 356/563 (63%), Positives = 420/563 (74%), Gaps = 12/563 (2%) Query: 2 ATVSGQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIF 61 + V + PM+ E++VIFASSLGTVFEWYDFYL GSLA+ I FFS T A IF Sbjct: 6 SAVRQHVEKRPMSSAERKVIFASSLGTVFEWYDFYLYGSLASIIGAQFFSQFPKTTADIF 65 Query: 62 TLLGFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASP 121 LL FAAGF VRPFGALVFGRLGD+VGRKYTFL+TI+IMGLST VVG LP Y +IG+A+P Sbjct: 66 ALLAFAAGFLVRPFGALVFGRLGDLVGRKYTFLVTILIMGLSTFVVGLLPNYDSIGIAAP 125 Query: 122 VIFIAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVR 181 +I I+ RLLQGLALGGEYGGAATYVAEHAP RRGFYT+WIQTTATLGLFLSLLVILG R Sbjct: 126 IILISARLLQGLALGGEYGGAATYVAEHAPHGRRGFYTSWIQTTATLGLFLSLLVILGTR 185 Query: 182 TAMGEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQ 241 T GE F GWR+PF+ S++LL +S+WIR+QL ESPAF ++K EG S+ PL+EAF Sbjct: 186 TFFGEARFAEIGWRVPFIVSVLLLLVSLWIRLQLSESPAFLKMKEEGTVSEKPLTEAFAT 245 Query: 242 WKNLKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFL 301 W N KI +LAL G+T GQ VVWYTGQFY+LFFL KVDG +AN+LIA AL+ GT FF+ Sbjct: 246 WSNAKIALLALFGLTMGQGVVWYTGQFYSLFFLQSICKVDGYTANLLIAWALVCGTGFFV 305 Query: 302 FFGSLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECS 361 FFG LSD IGRKPIIL GCL+AALTYFP+++A+T ANPAL A + + V+A+P +C Sbjct: 306 FFGWLSDHIGRKPIILTGCLLAALTYFPIYRAITANANPALAQALETVKVKVVADPADCG 365 Query: 362 FQFNPVGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDG-KAADA 420 FNPVGT FTSSCDIA+ L+K+ + Y+ V PAG+ AQI + +D + ++A Sbjct: 366 NLFNPVGTRVFTSSCDIARDFLAKSAVRYEMVPGPAGSPAQIVADGVNVTAFDSTQVSNA 425 Query: 421 KDAGKAFDKNLGTALKAASYPPKADPS--------QLNWPMT---VVILTILVIYVTMVY 469 K A F K AL+ A YP DP L+ P + +L ILVIYVTMVY Sbjct: 426 KTAMADFSKTATAALQEAGYPKPNDPGIIRMKHPFDLSEPRVLHLIGLLAILVIYVTMVY 485 Query: 470 GPIAAMLVEMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIA 529 GPIAA LVE+FPTRIRYTSMSLPYHIGNGWFGG LPATAFA+VA G+IY GLWYPII A Sbjct: 486 GPIAAALVELFPTRIRYTSMSLPYHIGNGWFGGLLPATAFAMVAQTGDIYYGLWYPIIFA 545 Query: 530 LATFVIGLLFVRETKDSNIYAQD 552 TFVIG LF+ ETKD +IYA+D Sbjct: 546 GITFVIGSLFIPETKDRDIYAED 568 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: 865 Number of extensions: 27 Number of successful extensions: 5 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: 568 Length adjustment: 36 Effective length of query: 516 Effective length of database: 532 Effective search space: 274512 Effective search space used: 274512 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