Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate Pf1N1B4_5596 Putative hydroxycinnamate transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5596 Length = 405 Score = 224 bits (572), Expect = 3e-63 Identities = 147/421 (34%), Positives = 216/421 (51%), Gaps = 34/421 (8%) Query: 24 SRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMSAALIGMVFGALG 83 SR + LCF++ ++G D A G A L Q + +D +G V SA +IG++ GA Sbjct: 5 SRRTTLTIALCFIVALIEGFDLQAAGTAAAGLRQTFALDPKMMGWVFSAGIIGLLPGAFF 64 Query: 84 SGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGLGAGMPNATTLLS 143 G +ADR GRK +L+GAVL+FG FSL++AY + LL+ RF+TGLGLGA +PN L + Sbjct: 65 GGWIADRIGRKKILIGAVLLFGVFSLSTAYVSTFSSLLLARFMTGLGLGAALPNLIALCA 124 Query: 144 EYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGGVLPLLLALVLMVW 203 E E+ + ++ M+ G LG A ++ M+ W + +IGG+ PLL+ ++++ Sbjct: 125 EAVGEQRRGTAISIMYAGVPLGGALAAVVA--MLFTDHWQATFIIGGLAPLLVVPLMILL 182 Query: 204 LPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAARSVFAVIFSGTYGL 263 LPES+ F + +GT VA S +F Sbjct: 183 LPESSAFR--QQQGTVN--------------------------VARASTGQALFGEGRAR 214 Query: 264 GTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFGGVLSAVGVGWAMD 323 T+ LWL+YF L ++Y+L +WLP+L+ + G S QA + LF GG L ++ G +D Sbjct: 215 ITLALWLSYFFTLTVMYMLLNWLPSLLLEQGFSKPQAGLVQMLFNIGGALGSLLGGLLLD 274 Query: 324 RYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGAQSAMPSLAARFYPT 383 R N KV+ Y V VG S+G I + AG+ V AQ + +LA YPT Sbjct: 275 RCNGIKVVLFVYAGLLVALAGVGLSVG-IVPMGIAGFAAGLFVMAAQLVLYALAPPSYPT 333 Query: 384 QGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTAL---LVPAALATVGVIVKG 440 RATGV + IGR G++ G + +L G VL A LV AAL + VI + Sbjct: 334 SVRATGVGAAVAIGRLGSVAGPLAAGQILTAGAGTTGVLLATSPGLVIAALTIISVIARS 393 Query: 441 L 441 + Sbjct: 394 V 394 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: 497 Number of extensions: 30 Number of successful extensions: 6 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: 405 Length adjustment: 32 Effective length of query: 416 Effective length of database: 373 Effective search space: 155168 Effective search space used: 155168 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