Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate PfGW456L13_2453 Major facilitator superfamily transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2453 Length = 558 Score = 781 bits (2017), Expect = 0.0 Identities = 379/548 (69%), Positives = 462/548 (84%), Gaps = 3/548 (0%) Query: 5 SGQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLL 64 +G + +T+EE++VIFASSLGTVFEWYDFYL GSLAA I+K FF+GVN T +FIF LL Sbjct: 9 TGSTPNRGLTREERKVIFASSLGTVFEWYDFYLYGSLAAIIAKHFFAGVNETTSFIFALL 68 Query: 65 GFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIF 124 FAAGFAVRPFGA+VFGRLGDM+GRK+TFLITIVIMG+ST VVG LPGYA IG+A+P+I Sbjct: 69 AFAAGFAVRPFGAIVFGRLGDMIGRKHTFLITIVIMGISTAVVGLLPGYATIGVAAPIIL 128 Query: 125 IAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAM 184 I++RLLQGLALGGEYGGAATYVAEHAP +RG++T+WIQTTATLGLFLSLLVIL RTA+ Sbjct: 129 ISLRLLQGLALGGEYGGAATYVAEHAPKGKRGYFTSWIQTTATLGLFLSLLVILACRTAL 188 Query: 185 GEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKN 244 G +AF AWGWRIPF+ S++LL ISV+IR+QL+ESP F ++KAEGK+SKAPL+E+F +W+N Sbjct: 189 GTEAFEAWGWRIPFLLSILLLIISVYIRLQLNESPVFVKMKAEGKSSKAPLTESFARWEN 248 Query: 245 LKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFG 304 LKIVI+AL+G TAGQAVVWYTGQFYALFFL QTLK++ +AN+LIA +LLIGTPFF+ FG Sbjct: 249 LKIVIMALLGGTAGQAVVWYTGQFYALFFLLQTLKIEPQTANLLIAGSLLIGTPFFVIFG 308 Query: 305 SLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQF 364 SLSDRIGRK II+AGC+IAALTYFP+F ALT Y NP + A +K+P+ V+ANP +CSFQF Sbjct: 309 SLSDRIGRKGIIMAGCIIAALTYFPIFHALTQYGNPDVFIAQEKNPVTVVANPAQCSFQF 368 Query: 365 NPVGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDG---KAADAK 421 +PVG +KFTSSCD+AK+ L+K + Y N A G +AQ+++GD I++++G AAD K Sbjct: 369 DPVGKAKFTSSCDLAKTVLAKRAIPYKNADAEPGAVAQVRIGDKVIESFEGTGMPAADFK 428 Query: 422 DAGKAFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFP 481 AF L TALK A YP KADP++ N+PM +++LTILVIYVTMVYGPIAA LVE+FP Sbjct: 429 AKNDAFATTLATALKDAGYPEKADPAKTNYPMVLLLLTILVIYVTMVYGPIAAWLVELFP 488 Query: 482 TRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVR 541 RIRYTSMSLPYHIGNGWFGGFLP AFA+VAA G+IY GLWYPI+IA+ T V+G+ F+ Sbjct: 489 ARIRYTSMSLPYHIGNGWFGGFLPTVAFAMVAATGDIYYGLWYPIVIAVMTAVLGIFFMP 548 Query: 542 ETKDSNIY 549 ETKD I+ Sbjct: 549 ETKDREIH 556 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: 899 Number of extensions: 39 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