Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate GFF1381 HP15_1348 major facilitator family transporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Marino:GFF1381 Length = 414 Score = 208 bits (530), Expect = 2e-58 Identities = 132/399 (33%), Positives = 204/399 (51%), Gaps = 19/399 (4%) Query: 19 ASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGAIVFGR 78 A G V+EWYDF ++G LA +A F+++ P +I G FA GF++RP GA VFG Sbjct: 2 AGFIGNVVEWYDFAVYGYLAGVIAPVFFSSANPTAALIGTYGIFAAGFIMRPLGAAVFGW 61 Query: 79 IGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQYGGA 138 GD GR T I++ +M T L+G+LP+ G A ++L+ +R+LQGL++GG++ + Sbjct: 62 FGDRYGRARTMQISVMLMALPTLLLGMLPSYQQAGLLAPVLLVLIRLLQGLSVGGEFSSS 121 Query: 139 ATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLPFMASI 198 AT++ E AP GKRG SW + G L+ + + +L E ++WGWRLPF+ Sbjct: 122 ATYLVETAPDGKRGLTGSWANIGSMTGSLLGVAAAALVTNTLDEQTLSDWGWRLPFLGGA 181 Query: 199 LLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATMGQGVV 258 +L I ++ IRR L S F Q + + +PL ++F N R L+AL A+ G Sbjct: 182 ILGIAAIAIRRNLHNSERFSQHHENRD-ETSPLLQAFTT--NRRETLLALAFAS-SYGTC 237 Query: 259 WYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFFGSLSDR-IGRKKVMLSGML 317 +Y Y +L + LI +LL +P F + DR + R+ + + Sbjct: 238 YYIVFVYLPEWLSAQELLSRGTALLINTGMMLLVIPAMPLFAIVGDRWLRRRSWIAISLF 297 Query: 318 LAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVYGPIAAFLV 377 L + +P++ M + + Y V+ LVF + + + G A V Sbjct: 298 LLTVVAWPLHAWMLSSGGS-----------LYVVVLAHALVF---LLLAIPLGSAPALFV 343 Query: 378 ELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATG 416 E+FP R + S+ +++G GVFGGL PMI LI TG Sbjct: 344 EMFPESDRLSGYSVAFNLGLGVFGGLTPMIATSLIATTG 382 Lambda K H 0.328 0.144 0.450 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: 565 Number of extensions: 35 Number of successful extensions: 4 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: 468 Length of database: 414 Length adjustment: 32 Effective length of query: 436 Effective length of database: 382 Effective search space: 166552 Effective search space used: 166552 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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