Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate BWI76_RS26970 BWI76_RS26970 aromatic acid/H+ symport family MFS transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__Koxy:BWI76_RS26970 Length = 452 Score = 481 bits (1239), Expect = e-140 Identities = 238/429 (55%), Positives = 323/429 (75%), Gaps = 2/429 (0%) Query: 11 SLDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVM 70 ++D+Q+FIN+ P ++YQW ++ LCF+ V +DG DTA +GFIA L QEWG+++++LGPVM Sbjct: 5 TIDIQAFINEHPFTKYQWMILALCFITVAMDGFDTAIIGFIASDLVQEWGVEKSALGPVM 64 Query: 71 SAALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLG 130 SAAL+G+ GAL +GPLADR GRK VL+ +++VFGGFSL +A+AT+++QL +LRFLTGLG Sbjct: 65 SAALVGLAVGALTAGPLADRVGRKKVLIMSIVVFGGFSLLTAFATSLNQLTLLRFLTGLG 124 Query: 131 LGAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGG 190 LGA MPNA TL+SEY PER ++L+V MF GF +G + GGF+SA MIP YGW S+LV+GG Sbjct: 125 LGAAMPNAATLMSEYAPERRRALMVNLMFVGFPMGSSLGGFLSAWMIPHYGWQSVLVLGG 184 Query: 191 VLPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAAR 250 V+PLLLA+VL+ LPESAR++VV+ + +I L IAP V E F + E + + Sbjct: 185 VMPLLLAVVLIFLLPESARYMVVKRQPAQRIAAILRRIAP--VPEQAEFELREAGQIQEK 242 Query: 251 SVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFG 310 S VIFS Y +GT++L LTYFMGL+I YLLTSWLP L+R++GA+M QA+ I ALF G Sbjct: 243 SSIGVIFSPRYAVGTIMLCLTYFMGLLIFYLLTSWLPLLIRETGATMSQASIITALFPLG 302 Query: 311 GVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGAQ 370 G + + +G MD+ NP+KV+ + +LL GVF VG S N+ ++ +V IAG +NGAQ Sbjct: 303 GGIGVLILGALMDKLNPNKVVAVGWLLTGVFVCLVGFSTHNLLLMGIMVFIAGSIMNGAQ 362 Query: 371 SAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPAA 430 S+MP+LAA FYPTQGRATGV+WMLGIGRFG ILGA+SGA L+ +FE + + L +PA Sbjct: 363 SSMPALAAGFYPTQGRATGVAWMLGIGRFGGILGAFSGAFLMQAQLSFETIFSLLAIPAF 422 Query: 431 LATVGVIVK 439 L+ + ++VK Sbjct: 423 LSAIALLVK 431 Lambda K H 0.325 0.140 0.424 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: 598 Number of extensions: 34 Number of successful extensions: 2 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: 448 Length of database: 452 Length adjustment: 33 Effective length of query: 415 Effective length of database: 419 Effective search space: 173885 Effective search space used: 173885 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: 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