Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate BPHYT_RS30250 BPHYT_RS30250 4-hydroxybenzoate transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__BFirm:BPHYT_RS30250 Length = 452 Score = 432 bits (1110), Expect = e-125 Identities = 209/429 (48%), Positives = 303/429 (70%), Gaps = 2/429 (0%) Query: 11 SLDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVM 70 +++VQ+FIN+ P S +QW V +CF+IV LDG DTAA+GFIAP+L EWGI R +L PV+ Sbjct: 6 AVNVQTFINEHPFSPFQWLVFFMCFIIVLLDGFDTAAIGFIAPSLIAEWGITRPALAPVL 65 Query: 71 SAALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLG 130 SAAL G+ GALGSGPL+DR GR+ +L+G+VL+FG L SA++T+++QL LRF+TG+G Sbjct: 66 SAALFGLACGALGSGPLSDRLGRRSLLLGSVLLFGVACLGSAFSTSIEQLTTLRFITGVG 125 Query: 131 LGAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGG 190 LGA MPNA T++ EY P+R ++ ++ MFCGF LG A GGF++A MIP +GW S+L++GG Sbjct: 126 LGAAMPNAVTMMGEYCPDRRRATVINLMFCGFPLGAAFGGFLAAWMIPHFGWRSVLLLGG 185 Query: 191 VLPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAAR 250 + PLLL +VL + +PES R++V N+ ++IR L+ I+ + A+AGSF + E Sbjct: 186 ITPLLLLIVLAIKMPESVRYMVANNKPVERIRAALARISSE-AAQAGSFVMTETAPQTGG 244 Query: 251 SVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFG 310 AV+ S +Y +G+++LW+ YFMGLVI Y +W+P L++D+G + ++A I ALF G Sbjct: 245 KGMAVVLSRSYIIGSVMLWIAYFMGLVIFYASINWMPILLKDAGLTPQRATLISALFPLG 304 Query: 311 GVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGAQ 370 GV AV G MDR+N +++I Y L V Y +GQ++GN+ L +V +AG+ +N AQ Sbjct: 305 GV-GAVLCGVLMDRFNANRIIAACYALTAVSVYFIGQAVGNVGALVFIVFVAGVLMNTAQ 363 Query: 371 SAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPAA 430 S+MP+LAA FYPT+GR TGV+WMLGIGRFG I G++ A L ++F + + V Sbjct: 364 SSMPALAAAFYPTEGRGTGVAWMLGIGRFGGIAGSFLVAELTRRHFSFAGIFAMVAVAGL 423 Query: 431 LATVGVIVK 439 LA + +++K Sbjct: 424 LACLALLIK 432 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: 593 Number of extensions: 34 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: 452 Length adjustment: 33 Effective length of query: 415 Effective length of database: 419 Effective search space: 173885 Effective search space used: 173885 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