Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate Pf1N1B4_4198 4-hydroxybenzoate transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4198 Length = 445 Score = 408 bits (1049), Expect = e-118 Identities = 208/431 (48%), Positives = 285/431 (66%), Gaps = 2/431 (0%) Query: 10 KSLDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPV 69 +++D++++I+ + ++ YQW ++ LCF IV DG D A MGFIAP+L QEWG+ +A GPV Sbjct: 4 ETVDIKAWIDNRKVAPYQWLIMGLCFFIVLFDGFDVAVMGFIAPSLIQEWGLSKAVFGPV 63 Query: 70 MSAALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGL 129 MSA ++G+ GAL +GP ADR GRK VL+ AV F SLA A+A N +L LR LTG+ Sbjct: 64 MSAGMVGLAIGALTAGPYADRLGRKKVLLTAVTGFSVLSLACAFARNPYELAALRLLTGV 123 Query: 130 GLGAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIG 189 LGA +PN TTLLSEY PER +SL +T MF GFN+G GGF++A +IP +GW S+L+ G Sbjct: 124 ALGAALPNTTTLLSEYLPERNRSLFITIMFTGFNMGSGLGGFLAAWLIPHHGWQSVLLAG 183 Query: 190 GVLPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAA 249 G+LPLLL ++ + LPESARFL RN +I K L+ + A A F + E +A Sbjct: 184 GILPLLLLPLMWLLLPESARFLAARNAPASQIAKVLNKLGGTFSA-ATKFVIAEPEA-QQ 241 Query: 250 RSVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQF 309 ++ ++F+ Y GT+ LW TYFMGL+++YL W+PTL+R+ G S+E+AA I LFQ Sbjct: 242 KAPLRLLFTEHYRFGTLALWATYFMGLLVIYLTMGWMPTLLREGGLSIERAATITGLFQI 301 Query: 310 GGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGA 369 GG + A+ VGWAMDR NP+ VI Y L G F +G ++LA V+ AG C++GA Sbjct: 302 GGTVGAIVVGWAMDRRNPNAVIATSYALGGAFILLLGAFSLESSLLAFGVVAAGFCMSGA 361 Query: 370 QSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPA 429 Q+ + + A +YPT RATGVSWMLGIGRFGAI G+ G +L LG + L VPA Sbjct: 362 QTGLNAFAPGYYPTDCRATGVSWMLGIGRFGAIFGSLIGGAVLSLGLGLPLLFALLSVPA 421 Query: 430 ALATVGVIVKG 440 +A + ++ G Sbjct: 422 FIAALAIMANG 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: 624 Number of extensions: 38 Number of successful extensions: 3 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: 445 Length adjustment: 33 Effective length of query: 415 Effective length of database: 412 Effective search space: 170980 Effective search space used: 170980 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