Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate SM_b20069 SM_b20069 amino acid carrier protein
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__Smeli:SM_b20069 Length = 467 Score = 614 bits (1583), Expect = e-180 Identities = 296/449 (65%), Positives = 367/449 (81%) Query: 1 MESLQKWVVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDES 60 ME+L ++ LNG+VWG M+VLI+GTGLYL L L FMP+ ++ GFR++ + R + Sbjct: 1 MEALNQFFNWLNGIVWGVPMIVLIIGTGLYLQLRLGFMPIRKVAYGFRMILKSRRPGRAA 60 Query: 61 SGEISPFQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAV 120 GEI+P+ ALMT L+AT+GTGNIAGVATAI +GGPGALFWMW TA VGMATK++EVV+AV Sbjct: 61 EGEITPYAALMTALSATIGTGNIAGVATAIAVGGPGALFWMWVTAFVGMATKYAEVVVAV 120 Query: 121 HYREKDERNEHVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEV 180 YRE D++ EH GGPM+AIKNGLGK W WLG AFA+FGGLAGFGIGNMVQ N +A A+E Sbjct: 121 KYREVDDKGEHAGGPMFAIKNGLGKHWQWLGTAFAIFGGLAGFGIGNMVQANGIASAVEN 180 Query: 181 SFGVPDWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPG 240 +FG+ W++G+ ++TG VILGGI+RIG VAE +VPFM + Y+V VLVV A IP Sbjct: 181 AFGIETWISGIVMTVLTGAVILGGIKRIGAVAEKVVPFMAIFYLVCVAAVLVVFAGNIPQ 240 Query: 241 AFQLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVR 300 A IFT AF+P AATGGF G+ V+ AIR GVARGIFSNEAGLGTAGIAQAAG+T + V Sbjct: 241 AIATIFTQAFSPTAATGGFLGSTVLMAIRMGVARGIFSNEAGLGTAGIAQAAGSTANPVF 300 Query: 301 SGLIGMLGTFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFEAAMPGVGHYILSLAL 360 SG+IGM+GTFIDT+I+C+LTGLAI+ SGVW SG +GA LSSAAFEAA+PG G+Y+++++L Sbjct: 301 SGVIGMMGTFIDTIIVCTLTGLAIMVSGVWASGETGAVLSSAAFEAALPGYGNYLVTISL 360 Query: 361 VVFAYTTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNAL 420 +FA+TTILGW+YY E+CWEYL GT + +PFRIVWT+A+ FGA LDFAWLVADTLNAL Sbjct: 361 ALFAFTTILGWAYYAEKCWEYLIGTASAIPFRIVWTVAVFFGATLSLDFAWLVADTLNAL 420 Query: 421 MAIPNLIALLLLSPVVFRLTREYFAKARS 449 MAIPNLI+LLLLSPV+ +LTR+YFA+ R+ Sbjct: 421 MAIPNLISLLLLSPVIAQLTRDYFAEERA 449 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: 737 Number of extensions: 43 Number of successful extensions: 1 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: 467 Length adjustment: 33 Effective length of query: 416 Effective length of database: 434 Effective search space: 180544 Effective search space used: 180544 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