Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate GFF3864 PGA1_78p00280 putative sodium/alanine symporter
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__Phaeo:GFF3864 Length = 458 Score = 593 bits (1530), Expect = e-174 Identities = 290/445 (65%), Positives = 353/445 (79%), Gaps = 1/445 (0%) Query: 1 MESLQKWVVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDES 60 ME L V +NG+VWGPLMLVLILG GL+L +GLK MP++R+G GF LL++GR D Sbjct: 1 MEVLNSIVGYINGIVWGPLMLVLILGVGLFLQIGLKLMPILRIGTGFALLFKGREAGD-G 59 Query: 61 SGEISPFQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAV 120 G+I+PF ALMT L+AT+GTGNIAGVATA+FLGGPGALFWMW TALVGMATK+SE VLAV Sbjct: 60 EGQITPFNALMTALSATIGTGNIAGVATAVFLGGPGALFWMWMTALVGMATKYSEAVLAV 119 Query: 121 HYREKDERNEHVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEV 180 YRE+D + +VGGPMY IKNGLG++WAWLG AFALFG +A FGIGN VQ N +A LE Sbjct: 120 KYREQDGQGNYVGGPMYYIKNGLGQKWAWLGFAFALFGAIAAFGIGNGVQANGVAQVLET 179 Query: 181 SFGVPDWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPG 240 +FG +TG+ M +TG VILGGI RIG VA LVPFM V YI ++VL+++A+ + Sbjct: 180 NFGFNPSITGIVLMALTGAVILGGITRIGAVAGKLVPFMAVSYITIGLLVLIINADQLGN 239 Query: 241 AFQLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVR 300 A L+FT+AFTP AA GGFAGAAV AAIRFGVARG+FSNEAGLG+A IA AA T V Sbjct: 240 ALGLVFTYAFTPSAAEGGFAGAAVWAAIRFGVARGVFSNEAGLGSAPIAHAAAETKGPVN 299 Query: 301 SGLIGMLGTFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFEAAMPGVGHYILSLAL 360 GLI MLGTFIDT+I+CS+TGLAII SG WTSG SGAAL+S AFE ++PG G Y++++AL Sbjct: 300 QGLIAMLGTFIDTIIVCSITGLAIIASGAWTSGESGAALTSLAFETSLPGFGGYVIAIAL 359 Query: 361 VVFAYTTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNAL 420 +FA+TTILGWSYYGE+C YL G + ++ +R++W +AI FGA L F WL+ADTLNA+ Sbjct: 360 SIFAFTTILGWSYYGEKCVGYLLGAKVLIGYRVLWIVAIYFGATADLGFIWLLADTLNAM 419 Query: 421 MAIPNLIALLLLSPVVFRLTREYFA 445 MAIPNLIAL LLSPVVF++T+E+FA Sbjct: 420 MAIPNLIALALLSPVVFKVTKEFFA 444 Lambda K H 0.326 0.140 0.437 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: 721 Number of extensions: 40 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: 449 Length of database: 458 Length adjustment: 33 Effective length of query: 416 Effective length of database: 425 Effective search space: 176800 Effective search space used: 176800 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 (21.7 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