Align 4-hydroxybenzoate transporter PcaK; 4-HB transporter (characterized)
to candidate AO356_29245 AO356_29245 MFS transporter
Query= SwissProt::Q43975 (457 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29245 Length = 447 Score = 215 bits (548), Expect = 2e-60 Identities = 133/435 (30%), Positives = 219/435 (50%), Gaps = 20/435 (4%) Query: 19 LDAQALINDAPLSRYQWLIAIVCFLIVFVDGIDTAAMGFIAPALAQDWGVDRSQLGPVMS 78 ++ AL D+ +R+ LI C LI+ +DG D A +G PA+ +D +D + G + Sbjct: 4 VNVYALAVDSTFNRFHGLILFWCVLILIIDGYDLAVVGAALPAIMKDMNIDPTSAGVMAG 63 Query: 79 AALGGMIIGALVSGPTADRFGRKIVLSMSMLVFGGFTLACAYSTNLDSLVIFRFLTGIGL 138 AAL G ++GA+ G ADR GR ++++ + +F FT A +++ S I RF+ G+G+ Sbjct: 64 AALFGTMLGAIFLGTLADRIGRPKMIAICVALFSIFTAAAGLTSDPISFSISRFVAGLGI 123 Query: 139 GAAMPNATTLFSEYCPARIRSLLVTCMFCGYNLGMAIGGFISSWLIPAFGWHSLFLLGGW 198 G +P T E+ P ++R+ LVT +F GY++G + LI ++GW +F + Sbjct: 124 GGVLPICTAQMGEFSPLKLRTRLVTLVFAGYSVGGILVALTGKQLIESYGWQWVFYV-AL 182 Query: 199 APLILMLLVIFFLPESYRFLIVKGKNTKKVRQILSRIAPQKVQGVTEFHVPEEKVEAGT- 257 P++L+ L++ +PES +L+ G+ +++R I +I P + E V G Sbjct: 183 LPVLLIPLILKTMPESIGYLLKTGRQ-EELRAIARKIDP-------TLQIDENTVMVGNA 234 Query: 258 -----KKGVFGMLFSAKYVKGTVLLWVTYFMGLVMIYLLTSWLPTLMRETGASLERAAFL 312 ++ LF TV++W + GL M+Y L SWL LM G SL A Sbjct: 235 AVLDKQQAPVRHLFKEGRGFSTVMIWAAFMTGLFMVYALNSWLTKLMAMAGFSLGSALNF 294 Query: 313 GGLFQFGGVLSALFIGWAMDRFNPNRIIAGFYLAAGIFAVIVGQSLSNPTLLALFILCAG 372 +F G ++ A+ GW D+ N ++ GFY+ I ++G + S TLL + G Sbjct: 295 VIVFNVGAIVGAIGGGWLSDKLNIKHVLVGFYIVGAIALTVLGYTRST-TLLFPVVFVVG 353 Query: 373 IAVNGAQSSMPVLSARFYPTQCRATGVAWMSGIGRFGAVFG----AWIGAVLLGNNWSFT 428 + G Q + FYP+ R+TGV + SG+GR GA+ W+ ++ L +F Sbjct: 354 ASTLGTQLLAYAYAGDFYPSTIRSTGVGFASGVGRIGAIVAPVLIGWLVSLNLPLEKNFM 413 Query: 429 MILSMLIIPAAAAAI 443 I +I AAA + Sbjct: 414 AISLAGLIGAAAVTL 428 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: 573 Number of extensions: 38 Number of successful extensions: 5 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: 447 Length adjustment: 33 Effective length of query: 424 Effective length of database: 414 Effective search space: 175536 Effective search space used: 175536 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