Align 4-hydroxybenzoate transporter PcaK; 4-HB transporter (characterized)
to candidate BPHYT_RS20015 BPHYT_RS20015 MFS transporter
Query= SwissProt::Q43975 (457 letters) >FitnessBrowser__BFirm:BPHYT_RS20015 Length = 415 Score = 210 bits (535), Expect = 6e-59 Identities = 141/410 (34%), Positives = 205/410 (50%), Gaps = 36/410 (8%) Query: 40 VCFLIVFVDGIDTAAMGFIAPALAQDWGVDRSQLGPVMSAALGGMIIGALVSGPTADRFG 99 +CF I ++G+D ++G AP +A+++G+ +Q+G SA G++ GA+ G ADR G Sbjct: 30 LCFAIALLEGLDLQSVGVAAPRMAREFGLSVAQMGLAFSAGTFGLLPGAMFGGRLADRIG 89 Query: 100 RKIVLSMSMLVFGGFTLACAYSTNLDSLVIFRFLTGIGLGAAMPNATTLFSEYCPARIRS 159 RK VL +S +FG ++ A ++ +LVI R LTGIGLG A+PN L SE R R Sbjct: 90 RKRVLVISACLFGLLSIMTALVSDFHTLVIVRVLTGIGLGGALPNLIALSSEAVEPRSRG 149 Query: 160 LLVTCMFCGYNLGMAIGGFISSWLIPAFGWHSLFLLGGWAPLILMLLVIFFLPESYRFLI 219 V+ M+CG G I I W +F +GG PL+L+ L++ FL +S F Sbjct: 150 TAVSVMYCGIPFGGVIASVIGVLSAGDTEWRHIFYVGGAGPLVLVPLLLVFLADSKAF-- 207 Query: 220 VKGKNTKKVRQILSRIAPQKVQGVTEFHVPEEKVEAGTKKGVFGMLFSAKYVKGTVLLWV 279 TK R + AP V +LF TV +WV Sbjct: 208 -----TKASRDGQVKPAP-----------------------VGEILFGGTRGLSTVQIWV 239 Query: 280 TYFMGLVMIYLLTSWLPTLMRETGASLERAAFLGGLFQFGGVLSALFIGWAMDRFNPNRI 339 +YF L+++Y L +WLP+LM +G + + ++ F GG + AL IG MDR + Sbjct: 240 SYFCTLIVLYFLLNWLPSLMAASGLTRAQVGYVQIFFNIGGGIGALCIGMLMDRMRSGVV 299 Query: 340 IAGFYLAAGIFAVIVGQSLSNP-TLLALFILCAGIAVNGAQSSMPVLSARFYPTQCRATG 398 +AG Y+ GI A + S ++ LA AG+ V G QS + LSA FYPT R TG Sbjct: 300 VAGMYV--GIIASLATLSTAHGFGALAASAFFAGMFVIGGQSVLYALSAAFYPTAMRGTG 357 Query: 399 VAWMSGIGRFGAVFGAWIGAVLLGNNWSFTMILSMLI---IPAAAAAIAI 445 V +GR G+V G LL S + ++ I + AAAAA+ + Sbjct: 358 VGAAVAVGRIGSVVGPLAAGQLLAMGRSSSTVIGASIPVTLIAAAAALLL 407 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: 505 Number of extensions: 33 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: 457 Length of database: 415 Length adjustment: 32 Effective length of query: 425 Effective length of database: 383 Effective search space: 162775 Effective search space used: 162775 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