Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate GFF3967 HP15_3907 sodium/alanine symporter family protein
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__Marino:GFF3967 Length = 453 Score = 638 bits (1645), Expect = 0.0 Identities = 304/450 (67%), Positives = 373/450 (82%), Gaps = 1/450 (0%) Query: 1 MESLQKWVVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSK-DDE 59 ME++ ++V +NG+VWGP MLVLILG GL+L LGLK MP+++LG GFRL+W+GRS E Sbjct: 1 MEAISEFVGQINGLVWGPPMLVLILGVGLFLSLGLKLMPVLKLGAGFRLMWKGRSAAGSE 60 Query: 60 SSGEISPFQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLA 119 S GEI PFQALMT L+ATVGTGNIAGVATA+FLGGPGALFWMW TALVGMATK+SE VLA Sbjct: 61 SEGEIPPFQALMTALSATVGTGNIAGVATAVFLGGPGALFWMWLTALVGMATKYSEAVLA 120 Query: 120 VHYREKDERNEHVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALE 179 V +RE DER HVGGPMY I+NGLG++WAWLG FA+F +AGFGIGN VQ NS+AD +E Sbjct: 121 VRFREVDERGAHVGGPMYYIRNGLGRKWAWLGVLFAVFAAIAGFGIGNTVQANSVADVME 180 Query: 180 VSFGVPDWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIP 239 +FG+P WVTG+ M++ G+V++GGIRRIG VA ALVP M V Y++A ++VL ++A IP Sbjct: 181 TNFGLPHWVTGLVLMVLVGMVLIGGIRRIGHVASALVPLMAVSYLLAGLVVLAINAADIP 240 Query: 240 GAFQLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAV 299 AF L+ HAF+PIAA GGFAGAAV AAIRFGVARGIFSNEAGLG+A IA AA T + + Sbjct: 241 AAFALVIKHAFSPIAAEGGFAGAAVWAAIRFGVARGIFSNEAGLGSAPIAHAAAQTRNPI 300 Query: 300 RSGLIGMLGTFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFEAAMPGVGHYILSLA 359 G++ MLGTFIDT+IIC++TGL IITSG WTSG SGAAL+S AF+ A+PGVG+Y++++A Sbjct: 301 NQGMVAMLGTFIDTIIICTITGLVIITSGTWTSGESGAALTSMAFQEALPGVGNYLVAIA 360 Query: 360 LVVFAYTTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNA 419 L VFA+TTILGWS+YGERC E+L G +AI+P+RI W LAIP GA L F WLVADTLNA Sbjct: 361 LAVFAFTTILGWSFYGERCIEFLFGVKAIVPYRIAWILAIPVGATLNLGFVWLVADTLNA 420 Query: 420 LMAIPNLIALLLLSPVVFRLTREYFAKARS 449 +MA+PNLIALL+LSP+VF+LTRE+F K ++ Sbjct: 421 MMALPNLIALLMLSPIVFKLTREHFEKEKA 450 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: 722 Number of extensions: 41 Number of successful extensions: 2 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: 453 Length adjustment: 33 Effective length of query: 416 Effective length of database: 420 Effective search space: 174720 Effective search space used: 174720 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