Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate BWI76_RS06435 BWI76_RS06435 MFS transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__Koxy:BWI76_RS06435 Length = 454 Score = 445 bits (1144), Expect = e-129 Identities = 214/430 (49%), Positives = 298/430 (69%), Gaps = 2/430 (0%) Query: 12 LDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMS 71 LDV+ IN PLSR+Q VVLL F ++ LDG D A MGFIAP L QEWG+ LG V+S Sbjct: 7 LDVRELINANPLSRFQKLVVLLGFCVIALDGFDIAIMGFIAPTLKQEWGVSNHELGFVIS 66 Query: 72 AALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGL 131 AALIG+ GA+ SGPLAD GRK +++ +V FG +++A+A + N++Q++V RFLTGLGL Sbjct: 67 AALIGLALGAIFSGPLADWLGRKKIIINSVFFFGFWTIATALSQNIEQMMVFRFLTGLGL 126 Query: 132 GAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGGV 191 GA MPN TL+SEY PER +S L+T +FCGF G A GGF ++ +IP +GWHSL+++GG+ Sbjct: 127 GAAMPNIGTLVSEYAPERQRSFLITIIFCGFTFGAAAGGFSASWLIPQFGWHSLMLLGGI 186 Query: 192 LPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAARS 251 LPLL A VL+ LPES RFLVV+ ++IR+ L + P + + FS+P Q A + Sbjct: 187 LPLLFAPVLIWLLPESVRFLVVKRAPAERIRRILQRLYPGQIPDEAEFSLPTQPVQA--N 244 Query: 252 VFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFGG 311 ++ S Y G+M+LWL YFMGL +VYLL SWLPTL+++ G ++ QAA + A++Q GG Sbjct: 245 AMRIVLSRQYRFGSMMLWLVYFMGLFLVYLLGSWLPTLVKEVGLTVSQAAVMTAMYQAGG 304 Query: 312 VLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGAQS 371 L ++ GW MDR NPH+ +G+ Y + G+F A+G + + ++ L I+G C+NGA + Sbjct: 305 TLGSLFAGWLMDRINPHRALGLIYAVGGLFTMAMGYAAASFALICLLAFISGACLNGANT 364 Query: 372 AMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPAAL 431 M +L+AR+YPT+ RATG SWM G+GR GAIL A++GA +L L +FE V L +PAA+ Sbjct: 365 GMNALSARYYPTEARATGSSWMHGVGRLGAILSAFAGAEMLALNISFESVFLILGIPAAI 424 Query: 432 ATVGVIVKGL 441 G+ KG+ Sbjct: 425 TVAGLAAKGV 434 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: 629 Number of extensions: 33 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: 454 Length adjustment: 33 Effective length of query: 415 Effective length of database: 421 Effective search space: 174715 Effective search space used: 174715 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