Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate AO356_27935 AO356_27935 3-phenylpropionic acid transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27935 Length = 407 Score = 228 bits (581), Expect = 3e-64 Identities = 142/413 (34%), Positives = 215/413 (52%), Gaps = 41/413 (9%) Query: 31 VLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMSAALIGMVFGALGSGPLADR 90 + LCF++ ++G D + G A L Q + +D +G V SA +IG++ GA G +ADR Sbjct: 12 IALCFIVALIEGFDLQSAGTAAAGLRQTFALDPKMMGWVFSAGIIGLLPGAFFGGWIADR 71 Query: 91 FGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGLGAGMPNATTLLSEYTPERL 150 GRK +L+ AVL+FG FSL++AY + LL++RF+TGLGLGA +PN L +E E+ Sbjct: 72 IGRKKILIAAVLLFGVFSLSTAYVEHFSSLLLVRFMTGLGLGAALPNLIALCAEAVGEQR 131 Query: 151 KSLLVTSMFCGFNLGMAGGGFISAKMIPAYG--WHSLLVIGGVLPLLLALVLMVWLPESA 208 + ++ M+ G L GG ++A + +G W IGG+ PLL+ ++++WLPES+ Sbjct: 132 RGTAISVMYAGVPL----GGALAAVVAMLFGEHWQMTFFIGGLAPLLVVPLMLLWLPESS 187 Query: 209 RFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAARSVFAVIFSGTYGLGTMLL 268 F V++ G+ + S +F G T+ L Sbjct: 188 AFRQVQDGGSSR-----------------------------GSTAQALFGEGRGRTTLAL 218 Query: 269 WLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFGGVLSAVGVGWAMDRYNPH 328 WL+YF L ++Y+L +WLP+L+ + G S QA + LF GG L ++ G +DR N Sbjct: 219 WLSYFFTLTVMYMLLNWLPSLLLEQGFSKPQAGLVQMLFNIGGALGSLLGGLLLDRCNGI 278 Query: 329 KVIGIFYLLAGVFAYAVGQSLG-NITVLATLVLIAGMCVNGAQSAMPSLAARFYPTQGRA 387 KV + ++ AG+ + G L I + AG+ V AQ + +LA YPT RA Sbjct: 279 KV--VLFVYAGLLSALAGVGLSVGIVPMGIAGFAAGLFVMAAQLVLYALAPPSYPTAVRA 336 Query: 388 TGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTAL---LVPAALATVGVI 437 TGV + IGR G++ G + +L G VL A LV A LA + VI Sbjct: 337 TGVGAAVAIGRLGSVAGPLAAGQILAAGGGTTAVLLATSPGLVVATLAVLSVI 389 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: 509 Number of extensions: 31 Number of successful extensions: 5 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: 407 Length adjustment: 32 Effective length of query: 416 Effective length of database: 375 Effective search space: 156000 Effective search space used: 156000 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