Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate RR42_RS30500 RR42_RS30500 4-hydroxybenzoate transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__Cup4G11:RR42_RS30500 Length = 447 Score = 392 bits (1007), Expect = e-113 Identities = 204/423 (48%), Positives = 279/423 (65%), Gaps = 4/423 (0%) Query: 11 SLDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVM 70 S+ + FI++QPLS +Q +V+LCFLIV +DG DTAA+GFIAPA+ EW + A L P+ Sbjct: 6 SIGITEFIDRQPLSAFQVTIVVLCFLIVAIDGFDTAAIGFIAPAIRAEWQLTPAHLAPLF 65 Query: 71 SAALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLG 130 A L G++ GA GPLADRFGRK VL+ VL FG SLA A++ ++ L+ LRFLTGLG Sbjct: 66 GAGLTGLMAGAFLFGPLADRFGRKNVLLFCVLFFGVASLACAFSGSLWGLVALRFLTGLG 125 Query: 131 LGAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGG 190 LG MPN TL SEY P + +S LVT+MFCGF +G A GG SA +I +GW ++L++GG Sbjct: 126 LGGAMPNTITLTSEYCPAKRRSFLVTTMFCGFTIGSALGGLASASLIEEHGWRAVLLLGG 185 Query: 191 VLPLLLALVLMVW-LPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAA 249 VLPLLL L L+VW LPES R+LV+ + +K+ L IAP+ GS V +++A Sbjct: 186 VLPLLL-LPLLVWKLPESVRYLVLSGKHPEKVAAILERIAPRERVAPGSIVVADKRAPG- 243 Query: 250 RSVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQF 309 S A +F GT+LLWLT+FM L+++YLL+SWLPTL+R +G S++ AA + +FQ Sbjct: 244 -SPVAHLFKPELVRGTLLLWLTFFMSLLVIYLLSSWLPTLLRATGISLKTAALVTMMFQV 302 Query: 310 GGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGA 369 GG L A+ +GW MDR NPH V+ Y LAGVF A+G + V AG C++G+ Sbjct: 303 GGTLGAIVLGWLMDRANPHYVLAASYALAGVFITAIGSLTTAPWLAGVAVFAAGFCISGS 362 Query: 370 QSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPA 429 Q +L+A +YPT RATGVSW G+GR G+++G+ G T+L +G + + +PA Sbjct: 363 QVGANALSAAYYPTDCRATGVSWANGVGRMGSVVGSVGGGTMLSMGLTMPALFLMVGIPA 422 Query: 430 ALA 432 +A Sbjct: 423 VMA 425 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: 604 Number of extensions: 35 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: 447 Length adjustment: 33 Effective length of query: 415 Effective length of database: 414 Effective search space: 171810 Effective search space used: 171810 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