Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate PP_2411 PP_2411 Major facilitator family transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__Putida:PP_2411 Length = 445 Score = 205 bits (522), Expect = 3e-57 Identities = 111/315 (35%), Positives = 175/315 (55%), Gaps = 4/315 (1%) Query: 18 KRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFAVRPFGA 77 +RVI AS++G EW+DF + G LA I+ FF+ + + A + T FA FA+RP G Sbjct: 13 RRVIAASAIGNFVEWFDFAVYGFLATLIASQFFASEDASVALLKTFAVFAVAFALRPLGG 72 Query: 78 LVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQGLALGG 137 +VFG LGD +GRK +TI++M ST ++G LP YA+IG+A+P + R LQG + GG Sbjct: 73 IVFGALGDRLGRKRILSLTILLMAGSTTLIGLLPTYASIGLAAPALLTLARCLQGFSAGG 132 Query: 138 EYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAWGWRIP 197 EY GA Y+ EHAP ++R FY +++ + + ++ G+ ++ +A AWGWRIP Sbjct: 133 EYAGACAYLMEHAPDDKRAFYGSFVPVSTFSAFACAAVIAYGLEASLSTEAMNAWGWRIP 192 Query: 198 FVASLVLLGISVWIRMQLHESPAFERIKAEGKTSK-APLSEAFGQWKNLKIVILALIGVT 256 F+ + L + +++R ++ E+PAF A+GK + +PL E + + A I +T Sbjct: 193 FLIAAPLGLVGLYLRWRMEETPAFREAVAQGKEHEHSPLKETLRHHGRVIRNLGAFISLT 252 Query: 257 AGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIGRKPII 316 A+ +Y Y +L + A + ++ +ALL G+ SDR+GR+ I Sbjct: 253 ---ALSFYMFTTYFATYLQLVGNLTRAQSLLVTTVALLFAAVGCPLAGAFSDRVGRRKTI 309 Query: 317 LAGCLIAALTYFPLF 331 CL L FP + Sbjct: 310 GFTCLWVMLCVFPAY 324 Score = 52.8 bits (125), Expect = 3e-11 Identities = 29/87 (33%), Positives = 50/87 (57%), Gaps = 2/87 (2%) Query: 453 MTVVILTILVIYVTMVYGPI--AAMLVEMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFA 510 M+ +L ++++ V + + AA+L E FPTR RYT+ ++ Y++ FGG P A Sbjct: 332 MSGALLGVILLAVGALCSGVVTAALLSESFPTRTRYTASAITYNVAYTLFGGTAPLVATW 391 Query: 511 IVAAKGNIYSGLWYPIIIALATFVIGL 537 ++A G+ + +Y ++IAL V GL Sbjct: 392 LIAQTGSSLAPAFYLVVIALVALVGGL 418 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: 601 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 552 Length of database: 445 Length adjustment: 34 Effective length of query: 518 Effective length of database: 411 Effective search space: 212898 Effective search space used: 212898 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