Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate CCNA_02495 CCNA_02495 4-hydroxybenzoate transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__Caulo:CCNA_02495 Length = 405 Score = 206 bits (524), Expect = 1e-57 Identities = 142/421 (33%), Positives = 201/421 (47%), Gaps = 42/421 (9%) Query: 31 VLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMSAALIGMVFGALGSGPLADR 90 V +C L+ +G D A G AP L+ + G+ LG S + G++ GA G L+DR Sbjct: 18 VAICCLLAVFEGFDLQAAGVAAPRLAPDLGLKPEDLGWFFSISTFGLMVGAALGGRLSDR 77 Query: 91 FGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGLGAGMPNATTLLSEYTPERL 150 FGRK L+ +V FG S+A+ A +++ LLV RFLTG+GLG +PN +++E +L Sbjct: 78 FGRKVTLLVSVAAFGLLSIATGLAQDLNGLLVARFLTGVGLGGALPNLIAIVAESVSPKL 137 Query: 151 KSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGGVLPLLLALVLMVWLPESARF 210 + V ++ G G A +S W + +GGV PLL L+ MV LP++ Sbjct: 138 RGRAVGFLYAGLPCGGALASLVSLAGADPSDWRIVFFVGGVGPLLAMLLAMVLLPDTPMA 197 Query: 211 LVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAARSVFAVIFSGT-YGLGTMLLW 269 V P+ Q +S F +G GL T+LLW Sbjct: 198 QV-------------GPVGDQ------------------KSGFVEALAGEGRGLTTLLLW 226 Query: 270 LTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFGGVLSAVGVGWAMD--RYNP 327 + +F+ L+I+YLL SWLP+LM G S A I F G +V GW MD R+ Sbjct: 227 IAFFLALLIMYLLLSWLPSLMIGRGLSRSDAGLIQMAFNLAGAAGSVATGWLMDHRRWRT 286 Query: 328 HKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGAQSAMPSLAARFYPTQGRA 387 ++G F A A A + ++ V + G V+G QS + LA FYP + R Sbjct: 287 LTILGAFGASAAAMATAAA-APASLAVFLIVGAALGATVSGVQSVVYGLAPGFYPARLRG 345 Query: 388 TGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPAALATVGVIVKGLVSHADA 447 TGV + +GR G+ G ATL+G G + QVL AL+ AL GLVS A Sbjct: 346 TGVGAAVVVGRLGSAAGPLLAATLIGAGGSSNQVLLALMPVIALG-------GLVSLLLA 398 Query: 448 T 448 T Sbjct: 399 T 399 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: 538 Number of extensions: 45 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: 405 Length adjustment: 32 Effective length of query: 416 Effective length of database: 373 Effective search space: 155168 Effective search space used: 155168 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