Align 4-hydroxybenzoate transporter PcaK; 4-HB transporter (characterized)
to candidate PP_3165 PP_3165 benzoate MFS transporter
Query= SwissProt::Q43975 (457 letters) >FitnessBrowser__Putida:PP_3165 Length = 442 Score = 266 bits (681), Expect = 8e-76 Identities = 151/434 (34%), Positives = 236/434 (54%), Gaps = 14/434 (3%) Query: 18 SLDAQALINDAPLSRYQWLIAIVCFLIVFVDGIDTAAMGFIAPALAQDWGVDRSQLGPVM 77 +LD +I++A + + W++ C L++ DG D G + P + ++WG+ Q G + Sbjct: 3 TLDVHPIIDNARFTPFHWMVMAWCGLLLIFDGYDLFIYGVVLPVIMKEWGLTPLQAGALG 62 Query: 78 SAALGGMIIGALVSGPTADRFGRKIVLSMSMLVFGGFTLACAYSTNLDSLVIFRFLTGIG 137 S AL GM+ GAL G ADR GRK +++ +F G T+ +++N I+RF+ G+G Sbjct: 63 SYALFGMMFGALAFGSLADRIGRKKGIAICFALFSGATILNGFASNPSEFGIYRFIAGLG 122 Query: 138 LGAAMPNATTLFSEYCPARIRSLLVTCMFCGYNLGMAIGGFISSWLIPAFGWHSLFLLGG 197 G MPNA L +EY P R+RS LV MF GY+LG + + +++P FGW S+F Sbjct: 123 CGGLMPNAVALMNEYAPKRLRSTLVAIMFSGYSLGGMLSAGVGIFMLPRFGWESMFFAAA 182 Query: 198 WAPLILMLLVIFFLPESYRFLIVKGKNTKKVRQILSRIAPQ-KVQGVTEFHVPEEKVEAG 256 PL+L+ +++++LPES FL+ +G+ ++ R +L R+ P VQ ++ ++A Sbjct: 183 -VPLLLLPVILYYLPESIGFLVRQGR-IEEARTLLKRLDPDCDVQA-------DDVLQAA 233 Query: 257 TKKGVFGM---LFSAKYVKGTVLLWVTYFMGLVMIYLLTSWLPTLMRETGASLERAAFLG 313 +KG LF T+ LWV +F L+M+Y L+SWLP LM G SL + Sbjct: 234 DRKGSGASVLELFRNGLAIRTLALWVAFFCCLLMVYALSSWLPKLMANAGYSLGSSLSFL 293 Query: 314 GLFQFGGVLSALFIGWAMDRFNPNRIIAGFYLAAGIFAVIVGQSLSNPTLLALFILCAGI 373 FGG+ A+ GW DR+N ++ F++AA + ++G + P +L L I AG Sbjct: 294 LALNFGGMAGAILGGWLGDRYNLVKVKVAFFIAAALSISLLGVNSPMP-VLYLLIFIAGA 352 Query: 374 AVNGAQSSMPVLSARFYPTQCRATGVAWMSGIGRFGAVFGAWIGAVLLGNNWSFTMILSM 433 G Q + +A+ Y R+TG+ W SGIGR GA+ G +G L+G N + Sbjct: 353 TTIGTQILLYAGAAQMYGLSVRSTGLGWASGIGRNGAIVGPLLGGALMGINLPLQLNFIA 412 Query: 434 LIIPAAAAAIAIFV 447 IP A AA+A+ V Sbjct: 413 FAIPGAIAALAMAV 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: 634 Number of extensions: 36 Number of successful extensions: 8 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: 442 Length adjustment: 33 Effective length of query: 424 Effective length of database: 409 Effective search space: 173416 Effective search space used: 173416 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