Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate PP_2569 PP_2569 Metabolite MFS transporter, MHS family
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__Putida:PP_2569 Length = 558 Score = 787 bits (2033), Expect = 0.0 Identities = 383/550 (69%), Positives = 464/550 (84%), Gaps = 3/550 (0%) Query: 2 ATVSGQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIF 61 +T +G +TKEE++VIFASSLGTVFEWYDFYL GSLAA I++ FF+GVN T +FIF Sbjct: 6 STSTGSAPQRGITKEERKVIFASSLGTVFEWYDFYLYGSLAAIIARHFFAGVNETTSFIF 65 Query: 62 TLLGFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASP 121 LL FAAGFAVRPFGA+VFGRLGDM+GRKYTFLITIVIMGLST VVG LPGYA IG+A+P Sbjct: 66 ALLAFAAGFAVRPFGAIVFGRLGDMIGRKYTFLITIVIMGLSTAVVGLLPGYATIGVAAP 125 Query: 122 VIFIAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVR 181 +I I +RLLQGLALGGEYGGAATYVAEHAP RRGF+TAWIQTTATLGLFLSLLVI+ R Sbjct: 126 IILITLRLLQGLALGGEYGGAATYVAEHAPKGRRGFFTAWIQTTATLGLFLSLLVIMACR 185 Query: 182 TAMGEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQ 241 TAMG +AF AWGWRIPF+ S++LL ISV+IR+QL+ESP F ++KAEGK SKAPL+E+F + Sbjct: 186 TAMGTEAFEAWGWRIPFLLSILLLAISVYIRLQLNESPVFMKMKAEGKASKAPLTESFAR 245 Query: 242 WKNLKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFL 301 W NLK+VI++L+G TAGQAVVWYTGQFYALFFL QTLK++ +AN+LIA +LLIGTPFF+ Sbjct: 246 WDNLKVVIMSLLGGTAGQAVVWYTGQFYALFFLLQTLKIEAQTANLLIAGSLLIGTPFFI 305 Query: 302 FFGSLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECS 361 FFGSLSDRIGRK II+AGC+IAALTYFP+FKALT Y NP + A +++P+VV+A+P +C+ Sbjct: 306 FFGSLSDRIGRKKIIMAGCIIAALTYFPIFKALTEYGNPDVFVAQEQNPVVVVADPGQCA 365 Query: 362 FQFNPVGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGK---AA 418 FQF+PVG +KFTSSCDIAKS L+K + Y N AA G++AQI++G+ + ++DG AA Sbjct: 366 FQFDPVGKAKFTSSCDIAKSLLAKRAIPYTNEAAEPGSVAQIRIGERVLPSFDGSSLAAA 425 Query: 419 DAKDAGKAFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVE 478 D K +AF L ALK A YP KAD +++++PM +++LTILVIYVTMVYGPIAA LVE Sbjct: 426 DFKVQSEAFTATLSGALKEAGYPEKADQAKIHYPMVLLLLTILVIYVTMVYGPIAAWLVE 485 Query: 479 MFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLL 538 +FP RIRYTSMSLPYHIGNGWFGGFLP AFA+VAA G+IY GLWYPI+IA+ T V+G+ Sbjct: 486 LFPARIRYTSMSLPYHIGNGWFGGFLPTVAFAMVAATGDIYYGLWYPIVIAVMTAVLGIF 545 Query: 539 FVRETKDSNI 548 F+ ETKD +I Sbjct: 546 FLPETKDRDI 555 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: 901 Number of extensions: 38 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: 558 Length adjustment: 36 Effective length of query: 516 Effective length of database: 522 Effective search space: 269352 Effective search space used: 269352 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