Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate N515DRAFT_0974 N515DRAFT_0974 MFS transporter, MHS family, proline/betaine transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__Dyella79:N515DRAFT_0974 Length = 433 Score = 168 bits (425), Expect = 4e-46 Identities = 105/332 (31%), Positives = 171/332 (51%), Gaps = 14/332 (4%) Query: 8 ISHAPMTKEEKRVIFA-SSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGF 66 ++ P T E R A ++L TV EWYDF L A +S+ FF G ++ + TL GF Sbjct: 1 MTEKPGTPEISRGSMAVAALSTVVEWYDFTLYLYFATVLSRVFFGGGE--SSLLATLAGF 58 Query: 67 AAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIA 126 A +A+RP GA+VFG +GD +GR+ T L+++++M L+ LP +A G A+ + + Sbjct: 59 AISYAMRPLGAVVFGHIGDRIGRRRTLLLSMMLMTLAMLATALLPSHAVAGPAAGALLLL 118 Query: 127 MRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGE 186 +R ++GGEY G Y+ E A +RRG T+ + +G L++ V +AM Sbjct: 119 LRCFMAFSVGGEYTGVVAYLLEGARKDRRGLITSLASAASEIGALLAVGVSALTVSAMST 178 Query: 187 DAFGAWGWRIPFVASLVLLGISVWI-RMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNL 245 +WGWRIPF L G VWI R + ESP F R + +PL N Sbjct: 179 AQLDSWGWRIPFFVGAALAG-CVWIARSTMEESPDFVRQVEQHTVPDSPLGHMLA---NH 234 Query: 246 KIVILALIGVTAGQAVVWYTGQFYALFFLTQT---LKVDGASANILIAIALLIGTPFFLF 302 + + ++A ++ +Y G Y FL+ + + + L A+A+++ TP Sbjct: 235 RPALFRTFAISALGSITYYVGITYVPAFLSSSGILAEERSLWLSTLAAVAVILVTP---L 291 Query: 303 FGSLSDRIGRKPIILAGCLIAALTYFPLFKAL 334 G+LSDR+GR+P+++ + + L +F+ + Sbjct: 292 AGALSDRVGRRPVLVWLAVASVLLPLAMFQLM 323 Score = 29.3 bits (64), Expect = 3e-04 Identities = 22/82 (26%), Positives = 34/82 (41%), Gaps = 3/82 (3%) Query: 435 LKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSMSLPYH 494 L A + A +LN + ++L L V+ V P A E FP R + ++L Sbjct: 315 LPLAMFQLMARAMELNIALGAIVLACLAGGVSAVGAPATA---EQFPGEGRLSGLALGVT 371 Query: 495 IGNGWFGGFLPATAFAIVAAKG 516 + FGG P A ++ G Sbjct: 372 MATAIFGGLTPFLAELLIKMTG 393 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: 540 Number of extensions: 27 Number of successful extensions: 5 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: 433 Length adjustment: 34 Effective length of query: 518 Effective length of database: 399 Effective search space: 206682 Effective search space used: 206682 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