Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate AO353_06120 AO353_06120 MFS transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__pseudo3_N2E3:AO353_06120 Length = 459 Score = 189 bits (479), Expect = 2e-52 Identities = 123/400 (30%), Positives = 201/400 (50%), Gaps = 17/400 (4%) Query: 18 INQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMSAALIGM 77 + + P+S Y + ++ L F D +D A M F+ ++ E+ + A G + S++ GM Sbjct: 12 LERLPISGYHRIIFIIIALAFFFDSMDLAMMTFLLGSIKAEFALSTAQAGLLASSSFFGM 71 Query: 78 VFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGLGAGMPN 137 V GA SG LADRFGRK V +++++G S + A +V+ L + R L G+G+G P Sbjct: 72 VLGASLSGMLADRFGRKPVFQWSIVLWGIASYLCSTAQSVETLTLFRVLLGIGMGMEFPI 131 Query: 138 ATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGGVLPLLLA 197 A ++LSE P + + + M + LG G +S ++P GW + ++ V P + Sbjct: 132 AQSMLSELIPAKRRGRYIALMDGFWPLGFVAAGVLSYFLLPLVGWRDIFLVLAV-PAVFV 190 Query: 198 LVLMVWLPESARFL--VVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQ---KAVAAR-- 250 L + ++PES R+L + DK+ L I +V GS +PE + +R Sbjct: 191 LAIRFFIPESPRWLEQAGHHAAADKV---LLRIEDKVRTSLGSADLPEPIRLPRIESRPG 247 Query: 251 ---SVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALF 307 S I+S Y TM++W +F L+ Y LTSWL L++ SG ++ Q+ + L Sbjct: 248 HFLSALNEIWSPLYRQRTMMIWSVWFFALLGFYGLTSWLSALLQQSGFAVTQSVYYTVLI 307 Query: 308 QFGGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSL---GNITVLATLVLIAGM 364 GG+ + W ++R+ V I L GV A+ GQS GN+++L + L+ Sbjct: 308 SLGGIPGFLMAAWLVERWGRKPVCIITLLGGGVMAFLYGQSAVFGGNVSLLISSGLLMQF 367 Query: 365 CVNGAQSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILG 404 + G + + + YPT RATG + IGR G++LG Sbjct: 368 FLFGMWAVLYTYTPELYPTSARATGSGFASAIGRVGSLLG 407 Lambda K H 0.325 0.140 0.424 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: 557 Number of extensions: 22 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: 448 Length of database: 459 Length adjustment: 33 Effective length of query: 415 Effective length of database: 426 Effective search space: 176790 Effective search space used: 176790 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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