Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate PP_0057 PP_0057 major facilitator family transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__Putida:PP_0057 Length = 539 Score = 674 bits (1739), Expect = 0.0 Identities = 324/543 (59%), Positives = 419/543 (77%), Gaps = 15/543 (2%) Query: 6 GQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLG 65 G + + +EE+++IFASSLGTVFEWYDF+L G+LAA ISK FF+GVN T AFIF L+ Sbjct: 9 GAAASSSSRREERKIIFASSLGTVFEWYDFFLYGALAAVISKQFFAGVNDTTAFIFALMA 68 Query: 66 FAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFI 125 FAAGF VRPFGALVFGRLGDM+GRKYTFL+TIV+MGLST VG LP YA+IG+A+P+I + Sbjct: 69 FAAGFLVRPFGALVFGRLGDMIGRKYTFLVTIVLMGLSTFAVGLLPTYASIGIAAPIILV 128 Query: 126 AMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMG 185 +R+LQGLALGGEYGGAATYVAEHAP +RG +T +IQ+TATLGL LSLLV+LG R G Sbjct: 129 ILRMLQGLALGGEYGGAATYVAEHAPPGKRGLHTGFIQSTATLGLLLSLLVVLGSRYISG 188 Query: 186 EDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNL 245 D F WGWR+PF+ S+VLL IS WIRM +HESPAF ++KA+GK SK+P+ E+F W NL Sbjct: 189 -DQFETWGWRLPFLLSIVLLAISTWIRMSMHESPAFVKMKAQGKVSKSPIRESFTSWPNL 247 Query: 246 KIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGS 305 K+V+ AL + AGQAV +YT QFY LFF+TQ LK+D A AN L+ I+++IG PFF+FFG Sbjct: 248 KVVLTALFSINAGQAVTFYTAQFYVLFFMTQMLKMDSAQANTLLIISVVIGAPFFVFFGW 307 Query: 306 LSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQFN 365 LSDRIGRKPI++ G L+A + YFPLFKAL+HYANP ++AA++++PIVV A+P C+FQF+ Sbjct: 308 LSDRIGRKPILMLGLLLATVLYFPLFKALSHYANPQIDAASRQAPIVVTADPQGCTFQFD 367 Query: 366 PVGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADAKDAGK 425 PVG ++F S CD K+ L K GL Y +V+ AG+ + +GD TI+ +D A A Sbjct: 368 PVGKARFDSPCDKVKTFLVKQGLPYSSVSV-AGSEVVVNIGDKTINGFDETAMRA----- 421 Query: 426 AFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIR 485 A++ A YP KADP+Q+N M VV++ +++ TM YGP+AA++VE+FPTRIR Sbjct: 422 --------AIEQAGYPAKADPAQVNQVMVVVLIVAMILIATMTYGPLAAVMVELFPTRIR 473 Query: 486 YTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVRETKD 545 YTSMSLPYHIGNGWFGGFLP +FA+V G+I+ GLWYP+++ + V+G+ +RETKD Sbjct: 474 YTSMSLPYHIGNGWFGGFLPTVSFALVVYTGDIFYGLWYPVLVTGISLVVGIFCLRETKD 533 Query: 546 SNI 548 +I Sbjct: 534 VDI 536 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: 799 Number of extensions: 37 Number of successful extensions: 10 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: 539 Length adjustment: 35 Effective length of query: 517 Effective length of database: 504 Effective search space: 260568 Effective search space used: 260568 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