Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate HSERO_RS00050 HSERO_RS00050 membrane protein
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__HerbieS:HSERO_RS00050 Length = 437 Score = 187 bits (476), Expect = 5e-52 Identities = 110/323 (34%), Positives = 170/323 (52%), Gaps = 19/323 (5%) Query: 17 EKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFAVRPFG 76 ++R + A+ +G EWYDF + G +A I++ FF N + + L F GF +RP G Sbjct: 7 KQRQVIAAIVGNALEWYDFIVYGFFSAIIARLFFPADNEYTSLLVALATFGIGFFMRPVG 66 Query: 77 ALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQGLALG 136 ++ G D GRK + IV+M L+ ++ F P YA IG+A+P++ + R+LQG A G Sbjct: 67 GVLLGLYADRKGRKAAMQVIIVLMTLAIAIIAFTPTYATIGIAAPIMIVVARMLQGFATG 126 Query: 137 GEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAWGWRI 196 GEY + ++ E APA++RG Y +W L +F + V + +A +WGWR+ Sbjct: 127 GEYSSSTAFLVESAPAHKRGLYGSWQLVGQCLAVFCGAGMGALVTRNLSPEALDSWGWRL 186 Query: 197 PFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVILALIGVT 256 PFV L++ + +WIR +HE+ F +++ K + AP+ K L +V L GV Sbjct: 187 PFVLGLLIGPVGLWIRRHMHETDDF--LESANKPNAAPI-------KLLDVVKTNLRGVL 237 Query: 257 AGQA-VVWYTGQFYALFFLTQT-------LKVDGASANILIAIALLIGTPFFLFFGSLSD 308 V+ T FY + T L +D A +IA+ALL T F G+LSD Sbjct: 238 VSMGQVINGTVAFYVVLVNMPTFANKQLGLPLDQAFMVQMIAVALL--TAVIPFAGALSD 295 Query: 309 RIGRKPIILAGCLIAALTYFPLF 331 R+GR+ ++L L L +PLF Sbjct: 296 RLGRRTVLLYSSLAFLLMVYPLF 318 Score = 51.2 bits (121), Expect = 8e-11 Identities = 24/78 (30%), Positives = 40/78 (51%) Query: 452 PMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAI 511 P +V+ +L I + +GP+ L E FPTR+R T +++ Y++ FGGF P + Sbjct: 328 PRLLVMQVLLCIVIGANFGPMPTALSEQFPTRVRSTGLAVAYNLAAMLFGGFAPFIVTWL 387 Query: 512 VAAKGNIYSGLWYPIIIA 529 G+ + WY + A Sbjct: 388 TKTSGSPVAPAWYVLFAA 405 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: 586 Number of extensions: 32 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: 437 Length adjustment: 34 Effective length of query: 518 Effective length of database: 403 Effective search space: 208754 Effective search space used: 208754 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