Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate HSERO_RS11125 HSERO_RS11125 major facilitator transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__HerbieS:HSERO_RS11125 Length = 553 Score = 814 bits (2103), Expect = 0.0 Identities = 398/552 (72%), Positives = 461/552 (83%), Gaps = 3/552 (0%) Query: 1 MATVSGQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFI 60 M T S + +T EEK+VIFASSLGTVFEWYDFYL GSLAA I+K FF+G +P AFI Sbjct: 1 MTTASVNTTARGITPEEKKVIFASSLGTVFEWYDFYLYGSLAAIIAKQFFAGTDPNTAFI 60 Query: 61 FTLLGFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMAS 120 F LL FAAGF VRPFGALVFGRLGD+VGRKYTFL+TI+IMG ST +VG LP Y +IG+ + Sbjct: 61 FALLAFAAGFIVRPFGALVFGRLGDLVGRKYTFLVTILIMGASTFIVGVLPNYNSIGITA 120 Query: 121 PVIFIAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGV 180 P+I I +R+LQGLALGGEYGGAATYVAEHAP RRG +TAWIQTTAT+GLFLSLLVILGV Sbjct: 121 PIILIILRILQGLALGGEYGGAATYVAEHAPEGRRGSFTAWIQTTATMGLFLSLLVILGV 180 Query: 181 RTAMGEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFG 240 RTA+GE AF WGWRIPF+ S++LL ISVWIRM ++ESPAF ++KAEGKTSKAPL+EAFG Sbjct: 181 RTAVGEAAFADWGWRIPFLVSILLLAISVWIRMSMNESPAFLKMKAEGKTSKAPLTEAFG 240 Query: 241 QWKNLKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFF 300 QWKNLK+VILAL+G+TAGQAVVWYTGQFYALFFLTQTLKVDG +ANILIA ALL+ TPFF Sbjct: 241 QWKNLKLVILALVGLTAGQAVVWYTGQFYALFFLTQTLKVDGPTANILIAAALLLATPFF 300 Query: 301 LFFGSLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDEC 360 LFFGSLSD+IGRKPIIL GCLIAA+TYFP+F LTH+ANPALEAA QKSP++V A+P C Sbjct: 301 LFFGSLSDKIGRKPIILGGCLIAAVTYFPIFSGLTHFANPALEAALQKSPVIVTADPASC 360 Query: 361 SFQFNPVGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADA 420 FQFNP GT KFTSSCDI K+ LS A +NY NVA G++A +K+GD I +YD Sbjct: 361 QFQFNPTGTKKFTSSCDIVKAKLSAASVNYQNVAGAPGSVATVKIGDRIITSYDAAGLSK 420 Query: 421 KDAG---KAFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLV 477 +DA K K+L +KAA YP KADP Q+N PM +++L ILVIYVTMVYGPIAA LV Sbjct: 421 EDAAAKDKQLSKDLADDIKAAGYPSKADPEQMNKPMVLLLLFILVIYVTMVYGPIAACLV 480 Query: 478 EMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGL 537 EMFPTRIRYTSMS+PYHIGNGWFGG LP T+FA+VA KG+IY GLWYPI+IA+ TFVIG+ Sbjct: 481 EMFPTRIRYTSMSMPYHIGNGWFGGLLPTTSFALVAFKGDIYYGLWYPIVIAMITFVIGM 540 Query: 538 LFVRETKDSNIY 549 LFV+ET +NI+ Sbjct: 541 LFVKETVRNNIH 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: 926 Number of extensions: 36 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: 553 Length adjustment: 36 Effective length of query: 516 Effective length of database: 517 Effective search space: 266772 Effective search space used: 266772 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