Align 4-hydroxybenzoate transporter PcaK; 4-HB transporter (characterized)
to candidate AO353_14270 AO353_14270 MFS transporter
Query= SwissProt::Q43975 (457 letters) >FitnessBrowser__pseudo3_N2E3:AO353_14270 Length = 447 Score = 274 bits (701), Expect = 4e-78 Identities = 156/431 (36%), Positives = 240/431 (55%), Gaps = 8/431 (1%) Query: 18 SLDAQALINDAPLSRYQWLIAIVCFLIVFVDGIDTAAMGFIAPALAQDWGVDRSQLGPVM 77 ++D +I++A +R+ W + C LI+ DG D G + P L +DWG+ Q G + Sbjct: 3 TIDVHEVIDNARFNRFHWRVLCWCALIIIFDGYDLVIYGVVLPMLMKDWGLSPLQAGALG 62 Query: 78 SAALGGMIIGALVSGPTADRFGRKIVLSMSMLVFGGFTLACAYSTNLDSLVIFRFLTGIG 137 S AL GM+ GAL GP +DR GRK +++ +++F GFT+ ++ N I RF+ G+G Sbjct: 63 SYALFGMMFGALFFGPLSDRIGRKKAITLCVMLFSGFTVLNGFAGNPTEFGICRFIAGLG 122 Query: 138 LGAAMPNATTLFSEYCPARIRSLLVTCMFCGYNLGMAIGGFISSWLIPAFGWHSLFLLGG 197 +G MPN L +EY P +IRS LV MF GY++G + + LIP+FGW S+F + Sbjct: 123 IGGVMPNVVALMNEYAPKKIRSTLVAIMFSGYSVGGMLSAGLGIVLIPSFGWQSVFYV-A 181 Query: 198 WAPLILMLLVIFFLPESYRFLIVKGKNTKKVRQILSRIAPQKV-QGVTEFHVPEEKVEAG 256 PL+L+ L++ FLPES F++ +G+N ++ R++L R+ P V Q + H+ E K G Sbjct: 182 IVPLLLLPLIMCFLPESVGFMLRQGRN-EQARKVLQRVDPAYVAQATDQLHMTEVK---G 237 Query: 257 TKKGVFGMLFSAKYVKGTVLLWVTYFMGLVMIYLLTSWLPTLMRETGASLERAAFLGGLF 316 + V LF T++LW+ +F L+ +Y L+SWLP LM G SL + + Sbjct: 238 SGTPVL-QLFREGRAMRTLMLWLAFFCCLLTVYALSSWLPKLMANAGYSLGSSLSFLLVL 296 Query: 317 QFGGVLSALFIGWAMDRFNPNRIIAGFYLAAGIFAVIVGQSLSNPTLLALFILCAGIAVN 376 FG + A+ G D+ N R++A F+ A + ++G + P +L L I AG Sbjct: 297 NFGAIFGAVGGGVLGDKLNLPRVLAVFFSIAAVSITLLGFNSPTP-VLYLLIAIAGATTI 355 Query: 377 GAQSSMPVLSARFYPTQCRATGVAWMSGIGRFGAVFGAWIGAVLLGNNWSFTMILSMLII 436 G+Q + +A+FY R+TG+ W SGIGR GA+ G +G LLG + + + Sbjct: 356 GSQILLYACAAQFYSMAIRSTGLGWASGIGRNGAIVGPLLGGALLGISLPLQLNFMAFAL 415 Query: 437 PAAAAAIAIFV 447 P A AAIA+ V Sbjct: 416 PGAIAAIAMAV 426 Lambda K H 0.328 0.141 0.438 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: 630 Number of extensions: 38 Number of successful extensions: 7 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: 457 Length of database: 447 Length adjustment: 33 Effective length of query: 424 Effective length of database: 414 Effective search space: 175536 Effective search space used: 175536 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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