Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate GFF696 PGA1_c07110 putative sodium/alanine symporter
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__Phaeo:GFF696 Length = 514 Score = 273 bits (697), Expect = 1e-77 Identities = 163/427 (38%), Positives = 234/427 (54%), Gaps = 33/427 (7%) Query: 50 LWQGRSKDDESSGEISPFQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGM 109 L +G D +GE+S FQAL T L+ TVG GNIAGVA A+ +GGPGA FWM L+GM Sbjct: 87 LVKGDYSDPNDAGEVSHFQALATALSGTVGLGNIAGVAVAVGIGGPGATFWMILAGLMGM 146 Query: 110 ATKFSEVVLAVHYREKDERNEHVGGPMYAIKNGLGKR----WAWLGAAFALFGGLAGFGI 165 A+KF+E L V YR + GGPMY + G R ++ F++F L FG Sbjct: 147 ASKFTECTLGVKYRNEYPDGTVSGGPMYYMTKGFAARGLPGGKFMAVLFSIFCILGAFGG 206 Query: 166 GNMVQVN-SMADALEVSFGVPDWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYI 224 GNM Q N + A V P W+TGV V VI+GG++ I V E +VPFM V Y+ Sbjct: 207 GNMFQANQAHAQLTNVLGDYPGWITGVIFAGVVFAVIIGGLKSIASVTEKVVPFMGVLYV 266 Query: 225 VASVIVLVVHAEAIPGAFQLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLG 284 + ++++++++ + I AF IF AFT + GG GA + G R FSNEAG+G Sbjct: 267 LTALVIILLNFDKIGWAFGQIFDGAFTGLGVAGGMVGALIQ-----GFKRAAFSNEAGVG 321 Query: 285 TAGIAQAAGTTHSAVRSGLIGMLGTFIDTLIICSLTGLAIITSGVWTS------------ 332 +A IA +A T + G + +L FIDT++IC++T L II +G S Sbjct: 322 SAAIAHSAVRTKEPITEGFVSLLEPFIDTVVICTMTALVIIITGQLVSDPETGLYVLNEA 381 Query: 333 --------GASGAALSSAAFEAAMPGVGHYILSLALVVFAYTTILGWSYYGERCWEYLAG 384 G SG AL+SAAF ++ G YIL++A+++FA++T++ WSYYG + W +L G Sbjct: 382 GSAIQTVDGNSGVALTSAAFSSSF-GWFKYILAIAVILFAFSTMISWSYYGLKAWTFLFG 440 Query: 385 TRAI--LPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPNLIALLLLSPVVFRLTRE 442 L F++++ L + GA L +D MA+ N++AL L P+V Sbjct: 441 ESKTTELVFKVIFCLFVIIGAAASLGPVIDFSDAAIFAMAVVNIVALYFLMPIVKGELNS 500 Query: 443 YFAKARS 449 Y A+ +S Sbjct: 501 YLARLKS 507 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: 626 Number of extensions: 35 Number of successful extensions: 7 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: 514 Length adjustment: 34 Effective length of query: 415 Effective length of database: 480 Effective search space: 199200 Effective search space used: 199200 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