Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate BWI76_RS19590 BWI76_RS19590 MFS transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__Koxy:BWI76_RS19590 Length = 452 Score = 367 bits (943), Expect = e-106 Identities = 181/427 (42%), Positives = 272/427 (63%), Gaps = 2/427 (0%) Query: 12 LDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMS 71 L++Q +N P+ QWRV++ CFL+V LDG DTAA+GFIAP + W + L P+ Sbjct: 5 LELQKLLNAAPVGARQWRVIICCFLVVMLDGFDTAAIGFIAPDIRSHWQLTAGDLAPLFG 64 Query: 72 AALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGL 131 A L+G+ GAL GPL+DRFGRK V+ V +FG FSL SA+A ++ L+ LRFLTGLGL Sbjct: 65 AGLLGLTAGALLCGPLSDRFGRKRVIEFCVALFGLFSLLSAFAPDLQMLVFLRFLTGLGL 124 Query: 132 GAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGGV 191 G MPN T+ SEY P R + LVT MFCGF LG A GG +SA+++P GWH +LV+GGV Sbjct: 125 GGAMPNTITMTSEYLPARRRGALVTLMFCGFTLGSAFGGVVSAQLVPLIGWHGILVLGGV 184 Query: 192 LPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAARS 251 LPL+LA+ L+ LPES R+ + R I +T+ I + + + ++ A A+ Sbjct: 185 LPLILAVALVPLLPESPRWQIRRQLPQATIARTVGAITGERYNDTHFWL--DEPAAGAKG 242 Query: 252 VFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFGG 311 + +F+G T++LW+ +FM L+I+YLL+SW+PTL+ G ++ A+++ A FQ GG Sbjct: 243 SISQLFAGRQLAITLMLWVVFFMSLLIIYLLSSWMPTLLNHRGIDLQHASWVTAAFQIGG 302 Query: 312 VLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGAQS 371 A+ +G MDR+NP++V+ + Y L V +G S + ++A + G+ ++G+Q Sbjct: 303 TFGALLLGVLMDRFNPYRVLALSYGLGAVCIVMIGLSENGLWLMALAIFGTGIGISGSQV 362 Query: 372 AMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPAAL 431 + +L A YPTQ RATGVSW +GR GAI+G+ SG ++ + ++F+ + + VPA + Sbjct: 363 GLNALTATLYPTQSRATGVSWSNAVGRCGAIVGSLSGGVMMAMNFSFDTLFFVIAVPAVV 422 Query: 432 ATVGVIV 438 + V +I+ Sbjct: 423 SAVMLIL 429 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: 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: 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