Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate GFF1317 PS417_06695 4-hydroxybenzoate transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__WCS417:GFF1317 Length = 446 Score = 798 bits (2061), Expect = 0.0 Identities = 398/444 (89%), Positives = 424/444 (95%) Query: 5 QNSVGKSLDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRA 64 Q SVG LDVQSFIN QPLSRYQWRVV+LCFLIVFLDGLDTAAMGFIAPALSQ+WGIDRA Sbjct: 3 QPSVGTPLDVQSFINAQPLSRYQWRVVILCFLIVFLDGLDTAAMGFIAPALSQDWGIDRA 62 Query: 65 SLGPVMSAALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLR 124 SLGPVMSAALIGMVFGALGSGPLADRFGRK VLVGAVLVFG FSLASAY++NVDQLLVLR Sbjct: 63 SLGPVMSAALIGMVFGALGSGPLADRFGRKVVLVGAVLVFGAFSLASAYSSNVDQLLVLR 122 Query: 125 FLTGLGLGAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHS 184 FLTGLGLGAGMPNATTLLSEYTPER KSLLVTSMFCGFNLGMAGGGFISAK+IPA+GWH+ Sbjct: 123 FLTGLGLGAGMPNATTLLSEYTPERHKSLLVTSMFCGFNLGMAGGGFISAKLIPAFGWHA 182 Query: 185 LLVIGGVLPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQ 244 LL+IGG+LPL+L +VLM+WLPESAR+LVVRNRGTDK+RKTLSPI P +V +A SFSVPEQ Sbjct: 183 LLLIGGILPLILVVVLMLWLPESARYLVVRNRGTDKVRKTLSPIDPVIVGQATSFSVPEQ 242 Query: 245 KAVAARSVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIG 304 K V AR+VFAVIFSGTY GT+LLWLTYFMGLVIVYLLTSWLPTLMRDSGAS+EQAAFIG Sbjct: 243 KTVKARNVFAVIFSGTYSAGTLLLWLTYFMGLVIVYLLTSWLPTLMRDSGASLEQAAFIG 302 Query: 305 ALFQFGGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGM 364 ALFQFGGVLSAVGVGWAMDR+NPHKVIG FYLLAGVFAYAVGQSLGNIT+LATLVLIAGM Sbjct: 303 ALFQFGGVLSAVGVGWAMDRFNPHKVIGSFYLLAGVFAYAVGQSLGNITLLATLVLIAGM 362 Query: 365 CVNGAQSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTA 424 CVNGAQSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAW GATLLGLGWNFEQVLTA Sbjct: 363 CVNGAQSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWMGATLLGLGWNFEQVLTA 422 Query: 425 LLVPAALATVGVIVKGLVSHADAT 448 L++PAALAT V++KG+VSHADAT Sbjct: 423 LVIPAALATAAVVIKGMVSHADAT 446 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: 785 Number of extensions: 41 Number of successful extensions: 3 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: 446 Length adjustment: 33 Effective length of query: 415 Effective length of database: 413 Effective search space: 171395 Effective search space used: 171395 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