Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate BPHYT_RS16375 BPHYT_RS16375 major facilitator transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__BFirm:BPHYT_RS16375 Length = 552 Score = 1008 bits (2605), Expect = 0.0 Identities = 497/552 (90%), Positives = 527/552 (95%) Query: 1 MATVSGQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFI 60 MATV GQISH PMT+EEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFI Sbjct: 1 MATVGGQISHVPMTREEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFI 60 Query: 61 FTLLGFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMAS 120 FTLL FAAGFAVRPFGA+VFGRLGDMVGRKYTFL+TIVIMGLST +VGFLPGYA+IG AS Sbjct: 61 FTLLSFAAGFAVRPFGAIVFGRLGDMVGRKYTFLVTIVIMGLSTFLVGFLPGYASIGFAS 120 Query: 121 PVIFIAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGV 180 PVIFIAMR+LQGLALGGEYGGAATYVAEHAPA RRGFYTAWIQTTATLGLFLSLLVILGV Sbjct: 121 PVIFIAMRMLQGLALGGEYGGAATYVAEHAPAGRRGFYTAWIQTTATLGLFLSLLVILGV 180 Query: 181 RTAMGEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFG 240 RTAMGEDAFG WGWRIPF+ S++LL +SVWIR+QLHESP FERIK+EGKTSKAPL+EAFG Sbjct: 181 RTAMGEDAFGDWGWRIPFIVSILLLAVSVWIRLQLHESPVFERIKSEGKTSKAPLTEAFG 240 Query: 241 QWKNLKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFF 300 QWKNLKIVILALIG+TAGQAVVWYTGQFY LFFLTQTLKVDG+SANI+IAIALLIGTPFF Sbjct: 241 QWKNLKIVILALIGLTAGQAVVWYTGQFYTLFFLTQTLKVDGSSANIMIAIALLIGTPFF 300 Query: 301 LFFGSLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDEC 360 LFFGSLSDRIGRKPII+AG LIAA TYFPLFKAL HY NPALEAAT K+PIVVIANPDEC Sbjct: 301 LFFGSLSDRIGRKPIIMAGLLIAACTYFPLFKALAHYTNPALEAATAKAPIVVIANPDEC 360 Query: 361 SFQFNPVGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADA 420 SFQFNPVGT+KFTSSCDIAKSALSKAGLNY+NVAAPAGTLAQIKVGDT I+TYDGKAADA Sbjct: 361 SFQFNPVGTAKFTSSCDIAKSALSKAGLNYENVAAPAGTLAQIKVGDTVINTYDGKAADA 420 Query: 421 KDAGKAFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMF 480 KD GKAFDK L T LK A Y PKADP+Q+NWPMTVVILTI++IYVTMVYGPIAAMLVEMF Sbjct: 421 KDQGKAFDKTLATTLKTAGYAPKADPTQINWPMTVVILTIMMIYVTMVYGPIAAMLVEMF 480 Query: 481 PTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFV 540 PTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNI+SGLWYPI+IAL TFVIG+LFV Sbjct: 481 PTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIFSGLWYPIVIALVTFVIGMLFV 540 Query: 541 RETKDSNIYAQD 552 RETKDS+IYA+D Sbjct: 541 RETKDSDIYAKD 552 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: 1069 Number of extensions: 36 Number of successful extensions: 3 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: 552 Length adjustment: 36 Effective length of query: 516 Effective length of database: 516 Effective search space: 266256 Effective search space used: 266256 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 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