Align 4-hydroxybenzoate transporter PcaK; 4-HB transporter (characterized)
to candidate Pf1N1B4_2832 benzoate MFS transporter BenK
Query= SwissProt::Q43975 (457 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2832 Length = 447 Score = 275 bits (704), Expect = 2e-78 Identities = 154/439 (35%), Positives = 245/439 (55%), Gaps = 8/439 (1%) Query: 19 LDAQALINDAPLSRYQWLIAIVCFLIVFVDGIDTAAMGFIAPALAQDWGVDRSQLGPVMS 78 +D +I++A +R+ W++ C LI+ DG D G + P L ++WG+ Q G + S Sbjct: 4 IDVHEVIDNARFNRFHWMVLFWCALIIIFDGYDLVIYGVVLPMLMKEWGLSPLQAGALGS 63 Query: 79 AALGGMIIGALVSGPTADRFGRKIVLSMSMLVFGGFTLACAYSTNLDSLVIFRFLTGIGL 138 AL GM+ GAL GP +D+ GRK +++ +++F GFT+ ++ N + RF+ G+G+ Sbjct: 64 YALFGMMFGALFFGPLSDKIGRKKAITLCVMLFSGFTVLNGFARNPTEFGLCRFIAGLGI 123 Query: 139 GAAMPNATTLFSEYCPARIRSLLVTCMFCGYNLGMAIGGFISSWLIPAFGWHSLFLLGGW 198 G MPN L +EY P +IRS LV MF GY++G + + LIP+FGW S+F + Sbjct: 124 GGVMPNVVALMNEYAPKKIRSTLVAIMFSGYSVGGMLSAGLGIVLIPSFGWQSVFYV-AV 182 Query: 199 APLILMLLVIFFLPESYRFLIVKGKNTKKVRQILSRIAPQKVQ-GVTEFHVPEEKVEAGT 257 PL+L+ L+++FLPES F++ +G+N ++ R +L R+ P V + H+ E K GT Sbjct: 183 LPLLLLPLIMYFLPESVGFMLRQGRN-QEARNVLERVDPAYVALASDQLHMSEVK---GT 238 Query: 258 KKGVFGMLFSAKYVKGTVLLWVTYFMGLVMIYLLTSWLPTLMRETGASLERAAFLGGLFQ 317 V LF T++LW+ +F L+M+Y L+SWLP LM G SL + + Sbjct: 239 GTPVL-QLFREGRALRTLMLWLAFFCCLLMVYALSSWLPKLMANAGYSLGSSLSFLLVLN 297 Query: 318 FGGVLSALFIGWAMDRFNPNRIIAGFYLAAGIFAVIVGQSLSNPTLLALFILCAGIAVNG 377 FG + A+ G D+ N R++A F++ A + ++G + P +L L I AG G Sbjct: 298 FGAIFGAVGGGVLGDKLNLPRVLAVFFVVAAVSITLLGFNSPMP-VLYLLIALAGATTIG 356 Query: 378 AQSSMPVLSARFYPTQCRATGVAWMSGIGRFGAVFGAWIGAVLLGNNWSFTMILSMLIIP 437 +Q + +A+FY R+TG+ W SGIGR GA+ G +G LLG + + +P Sbjct: 357 SQILLYACAAQFYSMTIRSTGLGWASGIGRNGAIVGPLLGGALLGISLPLQLNFMAFALP 416 Query: 438 AAAAAIAIFVKSLVAHTDA 456 A AA+A+ V ++ + A Sbjct: 417 GAVAALAMTVFAISSQRSA 435 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: 628 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