Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate WP_011386821.1 AMB_RS22655 MFS transporter
Query= SwissProt::Q51955 (448 letters) >NCBI__GCF_000009985.1:WP_011386821.1 Length = 453 Score = 265 bits (676), Expect = 3e-75 Identities = 147/431 (34%), Positives = 230/431 (53%), Gaps = 6/431 (1%) Query: 12 LDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMS 71 ++ I++ ++ W V+ LI+ DG D G + P L +EW +D G + S Sbjct: 4 VNAHKLIDEAKFGKFHWNVLFWTALIIIFDGYDLVIYGVVLPVLMKEWHLDPIQAGTLGS 63 Query: 72 AALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGL 131 AL GM+FGAL G L+DRFGRK V+ V++F F++ + + + + + RF+ GLG+ Sbjct: 64 YALFGMMFGALTFGSLSDRFGRKPVIAVCVVLFSLFTVLNGFVRDTTEFAICRFVAGLGI 123 Query: 132 GAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGGV 191 G MPNA L++EY P+RL+S LV MF G+++G + +IP YGW ++ + V Sbjct: 124 GGVMPNAVALMTEYAPKRLRSTLVAVMFSGYSVGGMLSAGLGMTLIPVYGWSAVFFVAAV 183 Query: 192 LPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAARS 251 PLLL V++ LPES FL+ R + K L+ + P + G + ++ Sbjct: 184 -PLLLLPVILFLLPESIGFLIKAGRTAEAADK-LARLEPSYKPQPGD-EISFPTGATGQA 240 Query: 252 VFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFGG 311 +F+G G+ T++ W+ +FM L++VY L SWLP LM ++G + + + FG Sbjct: 241 SLPALFAGGRGVSTVMFWIAFFMCLLMVYALGSWLPKLMNNAGYGLGSSLSFLLVLNFGA 300 Query: 312 VLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGAQS 371 + AVG G DR N +V+ F+++A + +G + VL LV +AG G Q Sbjct: 301 IFGAVGGGHIADRMNLKRVLVAFFVIAAISISLLGVKSPTL-VLYVLVAVAGATTIGTQI 359 Query: 372 AMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPAAL 431 + + A+FYP R+TG+ W G+GR GAILG G TLL Q A VP + Sbjct: 360 LLYAYVAQFYPMAIRSTGIGWASGVGRSGAILGPVLGGTLLAWKLPLMQNFMAFAVPGVI 419 Query: 432 ATV--GVIVKG 440 A + ++V+G Sbjct: 420 AAIAMSLVVRG 430 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: 623 Number of extensions: 33 Number of successful extensions: 7 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: 453 Length adjustment: 33 Effective length of query: 415 Effective length of database: 420 Effective search space: 174300 Effective search space used: 174300 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