Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate CCNA_00025 CCNA_00025 major facilitator superfamily transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__Caulo:CCNA_00025 Length = 550 Score = 573 bits (1477), Expect = e-168 Identities = 284/535 (53%), Positives = 372/535 (69%), Gaps = 7/535 (1%) Query: 18 KRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFAVRPFGA 77 + V+ ASS GT FEWYDF++ GSL ISK+FF+G+N TA +I L F GFA RP GA Sbjct: 12 RTVVSASSAGTAFEWYDFFIFGSLTQVISKTFFAGLNETAGYIAALALFGVGFAFRPLGA 71 Query: 78 LVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQGLALGG 137 LVFG++GD GRK FL T+++MG +T + FLP Y G+ +P++ I +R LQG ALGG Sbjct: 72 LVFGKIGDQDGRKGAFLATVLLMGGATFAIAFLPTYEQAGIIAPILLIILRCLQGFALGG 131 Query: 138 EYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGE----DAFGAWG 193 EYGGAA YVAEH+PAN+RG+ T+W+QT+A GLF +LLVIL R +G+ DAF WG Sbjct: 132 EYGGAAIYVAEHSPANKRGWATSWVQTSAAFGLFGALLVILATRWVLGKYVGPDAFDEWG 191 Query: 194 WRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVILALI 253 WRIPF SL LLGISVW+R++L ESP FE +KAEG+ SKAP +EAFGQW NLK+VILA + Sbjct: 192 WRIPFAVSLGLLGISVWMRLKLTESPTFEAMKAEGQASKAPYAEAFGQWSNLKLVILAFV 251 Query: 254 GVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIGRK 313 + Q VWYT FY F+ + LKVD + N L+ IA + F++ FG LSD++GRK Sbjct: 252 SMMCAQGAVWYTSFFYVQTFMEKFLKVDPVTINELMMIATAVSAIFYVVFGWLSDKVGRK 311 Query: 314 PIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQFNPVGTSKFT 373 P++L G +A L YFP F L ANPAL A+ K+P+VV A+P +CS QF+PVG + F Sbjct: 312 PVMLGGMTLALLFYFPGFHLLEKAANPALAEASAKAPVVVFADPKDCSLQFDPVGKTAFV 371 Query: 374 SSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTI--DTYDGKAADAKDAGKA-FDKN 430 +SCDI KS L+ AG++Y N AAPAG +A +++G + + G D A KA + Sbjct: 372 TSCDIVKSTLANAGVSYANEAAPAGAVAVMRIGGAEVLSKSAAGLGKDEVKATKAEVEGR 431 Query: 431 LGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSMS 490 + AL A YP KADP+++N PM + +L + VI T ++GP+AA LVE+FPTR+RYT++S Sbjct: 432 IKAALAGAGYPTKADPARMNMPMILGVLFVFVIAATALFGPLAACLVELFPTRVRYTALS 491 Query: 491 LPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVRETKD 545 LPYHIG GW GGF+P AFAIVAA GNIY+GLWYP L + + L + ETK+ Sbjct: 492 LPYHIGTGWVGGFVPFFAFAIVAAVGNIYAGLWYPFAFTLLSVLTTLFLLPETKE 546 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: 58 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: 550 Length adjustment: 36 Effective length of query: 516 Effective length of database: 514 Effective search space: 265224 Effective search space used: 265224 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