Align The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) (characterized)
to candidate GFF4482 PS417_22940 MFS transporter
Query= TCDB::Q7X4L6 (552 letters) >FitnessBrowser__WCS417:GFF4482 Length = 437 Score = 208 bits (530), Expect = 3e-58 Identities = 127/341 (37%), Positives = 189/341 (55%), Gaps = 11/341 (3%) Query: 1 MATIEGRAAPAPI-TSEERRVIFASSLGTVFEWYDFYL-AGSLAIYISRTFFSGVNPAAG 58 M+T AAPA T+ RV AS +GT E+YDFY+ A + A+ I FF + A Sbjct: 1 MSTTYNEAAPAAAPTNSTARVATASIVGTAIEFYDFYIYATAAALVIGPVFFPQTSGTAQ 60 Query: 59 FVFTLLGFAAGFAVRPFGAIVFGRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGM 118 + + L F F RP G+ +FG GD IGRK T +A++LLMG+ T ++GLLPGY +IG Sbjct: 61 MLASFLTFGIAFIARPLGSALFGHFGDRIGRKSTLVASLLLMGVCTTLIGLLPGYDSIGA 120 Query: 119 TAPVVFIAMRMLQGLALGGEYGGAATYVAEHAPSNKRGAWTAWIQTTATLGLFISLLVIL 178 AP++ +R QGL LGGE+GGAA E+AP KR + + Q ++G + + L Sbjct: 121 WAPILLCVLRFGQGLGLGGEWGGAALLATENAPKGKRAWFGMFPQLGPSIGFLAANGLFL 180 Query: 179 SVRSLLNEDTFAAWGWRVPFLVSIVLLAVSVWIRMQLHESPVFERIKAEGKTSKAPLSEA 238 + L+++ F +WGWR+PF++S L+ V ++ R++LHE+PVF A+ K PL E Sbjct: 181 ILAMSLSDEQFRSWGWRIPFILSAALVMVGLYARLKLHETPVFANAVAKEAPVKVPLVEL 240 Query: 239 FGQWKNLKIVLLALFGLTAGQAVVWYTGQFYTLFFLTQTLKVDGTSANMLVAVALL---I 295 F Q + VLL + A+ + T F +L + TL + L+ A+L + Sbjct: 241 FSQ--HWLPVLLGAASMVVCYALFYITTAF-SLSYGVSTLGYSRETFLGLLCFAVLFMGL 297 Query: 296 GTPFFLFFGSLSDKIGRKPIIMAGCLIAALTYFPLFKALAH 336 TP SD+ GRKP+++ G L+A L+ F + L H Sbjct: 298 ATPLAAL---ASDRFGRKPVLIVGALLAILSGFTMEPLLTH 335 Score = 48.5 bits (114), Expect = 5e-10 Identities = 28/89 (31%), Positives = 47/89 (52%), Gaps = 2/89 (2%) Query: 456 LILTILVLYVTMVYGPLAAMLVEMFPARIRYTSMSLPYHIGNGWFGGFLPATAFAIIAAR 515 L L + + + + + P+ AML E+FP R+RYT S Y++G P A ++A Sbjct: 343 LFLALELFLMGVTFAPMGAMLPELFPTRVRYTGASAAYNLGGIVGASAAPFFATKLVAMG 402 Query: 516 GNIYSGLWYPIVIASVAFVIGTLFVKETK 544 G Y G + + A++ +I L +KET+ Sbjct: 403 GLSYVGGY--VSAAALLSLIAVLCLKETR 429 Lambda K H 0.325 0.139 0.420 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: 641 Number of extensions: 28 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 552 Length of database: 437 Length adjustment: 34 Effective length of query: 518 Effective length of database: 403 Effective search space: 208754 Effective search space used: 208754 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