Align The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) (characterized)
to candidate PfGW456L13_1712 Permeases of the major facilitator superfamily
Query= TCDB::Q7X4L6 (552 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1712 Length = 445 Score = 206 bits (524), Expect = 2e-57 Identities = 117/328 (35%), Positives = 183/328 (55%), Gaps = 4/328 (1%) Query: 2 ATIEGRAAPAPITSEERRVIFASSLGTVFEWYDFYL-AGSLAIYISRTFFSGVNPAAGFV 60 +T + PA T+ RV AS +GT E+YDFY+ A + A+ I FF + A + Sbjct: 11 STTYSDSTPAQPTNSATRVATASFIGTAIEFYDFYVYATAAALVIGPVFFPQTSGTAQML 70 Query: 61 FTLLGFAAGFAVRPFGAIVFGRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGMTA 120 L F F RP G+ +FG GD IGRK T +A++LLMG+ T ++G+LPGY +IG A Sbjct: 71 SAFLTFGIAFLARPLGSALFGHFGDRIGRKSTLVASLLLMGVCTTLIGVLPGYDSIGAWA 130 Query: 121 PVVFIAMRMLQGLALGGEYGGAATYVAEHAPSNKRGAWTAWIQTTATLGLFISLLVILSV 180 P++ +R QGL LGGE+GGAA E+AP KR + + Q ++G + + L++ Sbjct: 131 PILLCVLRFGQGLGLGGEWGGAALLATENAPKGKRAWFGMFPQLGPSIGFLAANGLFLTL 190 Query: 181 RSLLNEDTFAAWGWRVPFLVSIVLLAVSVWIRMQLHESPVFERIKAEGKTSKAPLSEAFG 240 +L+++ F +WGWR+PFL+S L+ V +++R++LHE+PVF A + K PL E FG Sbjct: 191 AVVLDDEQFRSWGWRIPFLLSAALVMVGLYVRLKLHETPVFANAMARQERVKIPLFELFG 250 Query: 241 QWKNLKIVLLALFGLTAGQAVVWYTGQFYTLFFLTQTLKVDGTSANMLVAVALLIGTPFF 300 Q+ + +L G ++Y ++L + TL + L+ A+L Sbjct: 251 QY---WVPVLLGAGAMVVCYALFYISTVFSLSYGVATLGYSRETFLGLLCFAVLFMAAAT 307 Query: 301 LFFGSLSDKIGRKPIIMAGCLIAALTYF 328 SD+ GRKP+++ G ++A L+ F Sbjct: 308 PLSAWASDRYGRKPVLIIGGVLAILSGF 335 Score = 46.6 bits (109), Expect = 2e-09 Identities = 28/89 (31%), Positives = 46/89 (51%), Gaps = 2/89 (2%) Query: 456 LILTILVLYVTMVYGPLAAMLVEMFPARIRYTSMSLPYHIGNGWFGGFLPATAFAIIAAR 515 L L I + + + + P+ A+L E+FP +RYT S Y++G P A ++A Sbjct: 351 LFLCIELFLMGVTFAPMGALLPELFPTHVRYTGASAAYNLGGIVGASAAPFFAQKLVAMG 410 Query: 516 GNIYSGLWYPIVIASVAFVIGTLFVKETK 544 G Y G + + A+V +I L +KET+ Sbjct: 411 GLSYVGGY--VSAAAVLSLIAVLCLKETR 437 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: 603 Number of extensions: 32 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: 445 Length adjustment: 34 Effective length of query: 518 Effective length of database: 411 Effective search space: 212898 Effective search space used: 212898 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