Align 4-hydroxybenzoate transporter PcaK; 4-HB transporter (characterized)
to candidate PP_3740 PP_3740 Major facilitator family transporter
Query= SwissProt::Q43975 (457 letters) >FitnessBrowser__Putida:PP_3740 Length = 446 Score = 223 bits (569), Expect = 8e-63 Identities = 134/405 (33%), Positives = 211/405 (52%), Gaps = 6/405 (1%) Query: 22 QALINDAPLSRYQWLIAIVCFLIVFVDGIDTAAMGFIAPALAQDWGVDRSQLGPVMSAAL 81 Q L ND P+ R+Q L +C ++ +DG D M F A +++ +WG++ +Q+G ++SA L Sbjct: 7 QRLDND-PMGRFQCLAIGICIILNMIDGFDVLVMAFTAASVSAEWGLNGAQVGLLLSAGL 65 Query: 82 GGMIIGALVSGPTADRFGRKIVLSMSMLVFGGFTLACAYSTNLDSLVIFRFLTGIGLGAA 141 GM G+L P ADRFGR+ ++ + + + G L A S + L + R LTG+G+G Sbjct: 66 FGMAAGSLFIAPWADRFGRRPLILLCLALSGIGMLLSALSQSPLQLALLRGLTGLGIGGI 125 Query: 142 MPNATTLFSEYCPARIRSLLVTCMFCGYNLGMAIGGFISSWLIPAFGWHSLFLLGGWAPL 201 + ++ + SEY R R L V+ GY LG +GG ++ WL+ +GW S+FL GG + Sbjct: 126 LASSNVIASEYASERWRGLAVSLQSTGYALGATLGGLLAVWLLGHWGWRSVFLFGGVVTV 185 Query: 202 ILMLLVIFFLPESYRFLIVKGKNTKKVRQILSRIAPQKVQGVTEFHVPEEKVEAGTKKGV 261 +++ LV+ +LPES FL+ + R ++R+A + Q +P A K Sbjct: 186 LVIPLVLLWLPESLDFLLARRPANALAR--VNRLAVRLGQPALA-QLPAVAARAEGAKTG 242 Query: 262 FGMLFSAKYVKGTVLLWVTYFMGLVMIYLLTSWLPTLMRETGASLERAAFLGGLFQFGGV 321 F L + + T+++W+ +F+ + Y + SW P L+ G S ++ G L GG+ Sbjct: 243 FRQLLAPAMRRTTLVIWLLFFLVMFGFYFVMSWTPKLLVAAGLSAQQGITGGVLLSVGGI 302 Query: 322 LSALFIGWAMDRFNPNRIIAGFYL-AAGIFAVIVGQSLSNPTLLALFILCAGIAVNGAQS 380 + A IG R+ R++A F L A + + V S LAL +L G+ NG + Sbjct: 303 VGAALIGGLASRWPLTRVLALFMLITAALLVLFVANGASVTAALALGLL-IGLFSNGCVA 361 Query: 381 SMPVLSARFYPTQCRATGVAWMSGIGRFGAVFGAWIGAVLLGNNW 425 + LS Y RATGV W GIGR GA+ + VLL W Sbjct: 362 GLYALSPVVYDASVRATGVGWGIGIGRMGAILSPTVAGVLLDGGW 406 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: 620 Number of extensions: 41 Number of successful extensions: 3 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: 446 Length adjustment: 33 Effective length of query: 424 Effective length of database: 413 Effective search space: 175112 Effective search space used: 175112 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