Align 4-hydroxybenzoate transporter PcaK; 4-HB transporter (characterized)
to candidate BWI76_RS16895 BWI76_RS16895 3-(3-hydroxy-phenyl)propionate transporter MhpT
Query= SwissProt::Q43975 (457 letters) >FitnessBrowser__Koxy:BWI76_RS16895 Length = 398 Score = 201 bits (512), Expect = 3e-56 Identities = 130/410 (31%), Positives = 207/410 (50%), Gaps = 44/410 (10%) Query: 40 VCFLIVFVDGIDTAAMGFIAPALAQDWGVDRSQLGPVMSAALGGMIIGALVSGPTADRFG 99 +CF++ ++G+D A G A +AQ + +D+ Q+G + SA + G++ GAL G ADR+G Sbjct: 18 LCFMVALMEGLDLQAAGIAAVGMAQAFALDKMQMGWIFSAGILGLLPGALAGGMLADRYG 77 Query: 100 RKIVLSMSMLVFGGFTLACAYSTNLDSLVIFRFLTGIGLGAAMPNATTLFSEYCPARIRS 159 RK +L S+L+FG F++A A + N +L++ R LTG+GLGAA+PN L SE R R Sbjct: 78 RKRILLGSVLLFGLFSIATALAWNYPTLLLARLLTGVGLGAALPNLIALTSEAAGPRFRG 137 Query: 160 LLVTCMFCGYNLGMAIGGFISSWLIPAFGWHSLFLLGGWAPLILMLLVIFFLPESYRFLI 219 V+ M+CG +G A+ + + + A W ++F +GG PL+L+ L++ +LPES F Sbjct: 138 RAVSLMYCGVPIGAALAAALGFFGLAA-AWQTVFWVGGIVPLLLVPLLLRWLPESPVF-- 194 Query: 220 VKGKNTKKVRQILSRIAPQKVQGVTEFHVPEEKVEAGTKKGVFGMLFSAKYVKGTVLLWV 279 + QGV L + T+LLW+ Sbjct: 195 -----------------QRSAQGVP-----------------LRALLAPGNATATLLLWL 220 Query: 280 TYFMGLVMIYLLTSWLPTLMRETGASLERAAFLGGLFQFGGVLSALFIGWAMDRFNPNRI 339 YF L+++Y+L +WLP L+ G S AA + + QFG L +G MD+ +P + Sbjct: 221 CYFFTLLVVYMLINWLPMLLVGQGFSASEAAGVMFVLQFGAACGTLLLGALMDKLSP--L 278 Query: 340 IAGFYLAAGIFAVIVGQSLSNPTLLALFI---LCAGIAVNGAQSSMPVLSARFYPTQCRA 396 + +G+ A ++ +L T LA + AG+ G QS + L+ FY T+ RA Sbjct: 279 WMSLLIYSGMLASLL--ALGTATSLAAMLFSGFVAGLFATGGQSVLYALAPLFYRTEIRA 336 Query: 397 TGVAWMSGIGRFGAVFGAWIGAVLLGNNWSFTMILSMLIIPAAAAAIAIF 446 TGV IGR GA+ G + +L +++ A +A+F Sbjct: 337 TGVGTAVAIGRLGAMSGPLLAGKMLALGTGTVGVMAASAPGILLAGVAVF 386 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: 593 Number of extensions: 43 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 Length of query: 457 Length of database: 398 Length adjustment: 32 Effective length of query: 425 Effective length of database: 366 Effective search space: 155550 Effective search space used: 155550 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