Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate H281DRAFT_01185 H281DRAFT_01185 MFS transporter, AAHS family, 4-hydroxybenzoate transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__Burk376:H281DRAFT_01185 Length = 453 Score = 333 bits (853), Expect = 9e-96 Identities = 175/433 (40%), Positives = 265/433 (61%), Gaps = 3/433 (0%) Query: 10 KSLDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPV 69 K++DV+SFI+Q+PL + + +L FL + LDGLDT+AMG IAP L ++WG+ ++ L PV Sbjct: 2 KTIDVKSFIDQRPLKPFHAILFMLMFLTIVLDGLDTSAMGLIAPTLMKQWGVTKSDLAPV 61 Query: 70 MSAALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGL 129 +SAAL+G+ GA+ PLADR GR+ VLV +V FG FS+A+ +TNV +L+ R LTG+ Sbjct: 62 LSAALVGIGIGAIFGAPLADRIGRRVVLVTSVAFFGVFSIAAGCSTNVTELMWSRLLTGV 121 Query: 130 GLGAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIG 189 GLGA +P TL++E+ P R++S V M GF +G G ++ +IP +GW L++G Sbjct: 122 GLGAAIPLCATLVNEFLPSRMRSRAVNFMLFGFAVGGGITGPLAKSVIPTHGWEGYLIVG 181 Query: 190 GVLPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAA 249 GV P+++A++L +LPES R+L +G DKI K L I P +F V E A Sbjct: 182 GVAPIVVAVLLAFFLPESVRYLAAAGKGQDKIVKALKRIDPTADFTDTTF-VAEVSAAVQ 240 Query: 250 RSVFAV--IFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALF 307 + F V +FS TMLLW+ Y + +Y+L+ WLPT+++ G ++ Q A F Sbjct: 241 KRKFPVSELFSARLRWPTMLLWVAYICSTITLYVLSMWLPTILQGDGRTLAQTANTMMWF 300 Query: 308 QFGGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVN 367 + + + G MD++ P +VI ++ ++ A V S + L TL++IA M N Sbjct: 301 NWCSGAAILLAGVLMDKFGPVRVISAYFAISMSMALLVSISGAHGDALLTLLVIAAMTNN 360 Query: 368 GAQSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLV 427 GA S+M +LA + YPT RATG +W+LG+GRFG I G + G ++GLGW ++ + + Sbjct: 361 GACSSMSTLATQMYPTSSRATGAAWVLGVGRFGGIAGTFLGPVMIGLGWPLTTIVAWIAL 420 Query: 428 PAALATVGVIVKG 440 PA +A+V + G Sbjct: 421 PAVIASVSIFCIG 433 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: 549 Number of extensions: 29 Number of successful extensions: 4 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