Align 4-hydroxybenzoate transporter PcaK; 4-HB transporter (characterized)
to candidate HSERO_RS06575 HSERO_RS06575 major facilitator transporter
Query= SwissProt::Q43975 (457 letters) >FitnessBrowser__HerbieS:HSERO_RS06575 Length = 455 Score = 271 bits (694), Expect = 2e-77 Identities = 148/430 (34%), Positives = 234/430 (54%), Gaps = 10/430 (2%) Query: 18 SLDAQALINDAPLSRYQWLIAIVCFLIVFVDGIDTAAMGFIAPALAQDWGVDRSQLGPVM 77 +LD +I+ A +++ W++ +C L++ DG D G + P L ++W + Q G + Sbjct: 3 TLDVSQIIDGARFTKFHWMVMCLCALLLVFDGYDLFIYGAVLPVLMKEWSLSPVQAGALG 62 Query: 78 SAALGGMIIGALVSGPTADRFGRKIVLSMSMLVFGGFTLACAYSTNLDSLVIFRFLTGIG 137 S AL GM+ GA + GP ADR GRK +++S ++F T ++T+ ++RFL G+G Sbjct: 63 SYALFGMMFGAFIFGPLADRIGRKKGVAISFVLFSVSTFLSGFATSPTEFGVYRFLAGLG 122 Query: 138 LGAAMPNATTLFSEYCPARIRSLLVTCMFCGYNLGMAIGGFISSWLIPAFGWHSLFLLGG 197 G MPNA L +EY P R+RS LV MF GY+LG + + W++P FGW S+F Sbjct: 123 CGGLMPNAVALMNEYAPKRLRSTLVAIMFSGYSLGGVLCAGLGIWMLPNFGWQSMFFAAA 182 Query: 198 WAPLILMLLVIFFLPESYRFLIVKGKNTKKVRQILSRIAPQKVQGVTEFHVPEEKVEAGT 257 PL+L+ ++++ LPES FL+ +G+ ++ R +L+++ PQ + V+A Sbjct: 183 -VPLVLLPVILWKLPESVGFLLRQGR-LEQARAMLTQVDPQ-----ARIATDTQLVQADV 235 Query: 258 KKGVFGM--LFSAKYVKGTVLLWVTYFMGLVMIYLLTSWLPTLMRETGASLERAAFLGGL 315 K M LF GT+++WV++F L+M+Y L SWLP LM G SL + Sbjct: 236 KGAGAPMLHLFKQDRAVGTLMIWVSFFCCLLMVYALGSWLPKLMASAGYSLGSSLSFLLA 295 Query: 316 FQFGGVLSALFIGWAMDRFNPNRIIAGFYLAAGIFAVIVGQSLSNPTLLALFILCAGIAV 375 FGGV+ A+ GW DRF +++ F+ + ++G + P +L L I+ AG Sbjct: 296 LNFGGVVGAIGGGWLGDRFTLPKVVVSFFTVGTVAIALLGFNSPTP-VLYLLIIVAGATT 354 Query: 376 NGAQSSMPVLSARFYPTQCRATGVAWMSGIGRFGAVFGAWIGAVLLGNNWSFTMILSMLI 435 G Q + +A+FYP R+TG+ W SG+GR GA+ G +G L+ M + Sbjct: 355 IGTQILLYANTAQFYPLAIRSTGLGWASGVGRSGAIVGPLLGGALMAAALPLKMNFLVFA 414 Query: 436 IPAAAAAIAI 445 IP AA+A+ Sbjct: 415 IPGLVAALAM 424 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: 686 Number of extensions: 47 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: 455 Length adjustment: 33 Effective length of query: 424 Effective length of database: 422 Effective search space: 178928 Effective search space used: 178928 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