Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate Ga0059261_0987 Ga0059261_0987 MFS/sugar transport protein/Sugar (and other) transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__Korea:Ga0059261_0987 Length = 533 Score = 441 bits (1133), Expect = e-128 Identities = 237/547 (43%), Positives = 334/547 (61%), Gaps = 26/547 (4%) Query: 1 MATVSGQI--SHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAA--FISKSFFSGVNPT 56 MAT I H P E ++V+ ASSLGTVFEWYDF++ G+LAA I ++FF+ NP Sbjct: 1 MATTVEDIRPEHEPSKSEMRQVVTASSLGTVFEWYDFFIYGTLAASGVIGRTFFATGNPV 60 Query: 57 AAFIFTLLGFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAI 116 ++ GFA GF RP GA++FG LGD +GRKYTFL+TI +MG++T VGF+P YA+I Sbjct: 61 LETLYAWAGFAVGFGFRPLGAVLFGYLGDKLGRKYTFLVTITLMGVATAGVGFVPSYASI 120 Query: 117 GMASPVIFIAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLV 176 G A+P I I +R+LQGLALGGEYGGAA YV+EH+P + G++T++IQ + + G LSL V Sbjct: 121 GAAAPAIVIGLRILQGLALGGEYGGAAIYVSEHSPTGQAGYHTSFIQASVSAGFILSLAV 180 Query: 177 ILGVRTAMGEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLS 236 +L R M + +F WGWR+PF+ S+ LL IS+W+R++L ESP F+ +K G+ ++ PL Sbjct: 181 VLITRFTMPQASFDDWGWRLPFIFSIALLAISLWMRVKLSESPVFKAMKEAGEVARNPLK 240 Query: 237 EAFGQWKNLKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIG 296 E+F NL+ + +AL G+ AG V+WYT F L FL T++V+ +A +L A G Sbjct: 241 ESFTYPGNLRRLFVALFGIAAGLTVIWYTATFSVLSFLQGTMRVEPVAAQLLAAGGAAAG 300 Query: 297 TPFFLFFGSLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIAN 356 +F+ FG LSDRIGRK I+ G L FP+F A+ H ANPAL A + +P++V + Sbjct: 301 LFWFILFGKLSDRIGRKKPIVIGYGFTLLLLFPIFWAMGHAANPALSDAARNAPVIV--S 358 Query: 357 PDECSFQFNPVGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGK 416 +C+ ++P K +C LSK G+ Y P+ ++ V + +T D Sbjct: 359 GPQCA--YDPF-AGKQADTCGQLLDYLSKKGVPYTKEVTPSAAVSVNGVPVISTETAD-- 413 Query: 417 AADAKDAGKAFDKNLGTALKAASYP-PKADPSQLNWPMTVVILTILVIYVTMVYGPIAAM 475 + AL A Y + PS N + ++ + L YGP+AA+ Sbjct: 414 --------------IDKALTEAGYNLDRVVPSTGNIVLILIAIVALAALSGATYGPVAAL 459 Query: 476 LVEMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVI 535 L E+FP RIRY+SMS+PYHIG G+FGGFLP + +VA GN YSGLWY I+ ++ Sbjct: 460 LTELFPPRIRYSSMSIPYHIGTGYFGGFLPLISQYMVAKSGNAYSGLWYTWIVVAMALLV 519 Query: 536 GLLFVRE 542 L F+RE Sbjct: 520 TLFFLRE 526 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: 806 Number of extensions: 40 Number of successful extensions: 6 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: 533 Length adjustment: 35 Effective length of query: 517 Effective length of database: 498 Effective search space: 257466 Effective search space used: 257466 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