Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate GFF2091 Psest_2134 amino acid carrier protein
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__psRCH2:GFF2091 Length = 447 Score = 730 bits (1885), Expect = 0.0 Identities = 353/447 (78%), Positives = 403/447 (90%) Query: 1 MESLQKWVVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDES 60 ME L V +NG+VWGP MLVLILGTGL+LM+ LKFMPL R+ GF L+W+GR+K DE+ Sbjct: 1 MEFLNNLVNSVNGLVWGPPMLVLILGTGLFLMIFLKFMPLTRIPTGFALMWRGRTKGDEA 60 Query: 61 SGEISPFQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAV 120 +GEISPFQALMT LAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATK+ EVVLAV Sbjct: 61 TGEISPFQALMTSLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKYCEVVLAV 120 Query: 121 HYREKDERNEHVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEV 180 HYREKD+R EHVGGPMYAIKNGLGK+W WLG AFA+FGGLAGFGIGNMVQVNSMA ALE Sbjct: 121 HYREKDDRGEHVGGPMYAIKNGLGKKWIWLGTAFAIFGGLAGFGIGNMVQVNSMAHALET 180 Query: 181 SFGVPDWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPG 240 +F VP W TG+ TM++ GLVILGGIRRIG VA +LVPFMC+ Y++A+ +VLVV+ AIP Sbjct: 181 TFAVPLWATGLVTMVIVGLVILGGIRRIGVVAASLVPFMCLAYLIAAAVVLVVNVSAIPA 240 Query: 241 AFQLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVR 300 AF LIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTT S+VR Sbjct: 241 AFDLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTTSSVR 300 Query: 301 SGLIGMLGTFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFEAAMPGVGHYILSLAL 360 SG+IGMLGTFIDT+I+CS+TGLAII +GVWTSG SGAALS+AAFE+AMPG+G IL++AL Sbjct: 301 SGMIGMLGTFIDTIIVCSMTGLAIICTGVWTSGESGAALSAAAFESAMPGIGGIILTIAL 360 Query: 361 VVFAYTTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNAL 420 VVFA+TTILGWSY+GE+CWE+L GTRAI PFR++W LA+PFGA+ QLDFAWL+ADTLN L Sbjct: 361 VVFAFTTILGWSYFGEKCWEFLVGTRAIWPFRVIWVLAVPFGAIAQLDFAWLLADTLNGL 420 Query: 421 MAIPNLIALLLLSPVVFRLTREYFAKA 447 MAIPNLI+LLLLSPVV +LT+EYFA++ Sbjct: 421 MAIPNLISLLLLSPVVVKLTKEYFARS 447 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: 799 Number of extensions: 38 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: 447 Length adjustment: 33 Effective length of query: 416 Effective length of database: 414 Effective search space: 172224 Effective search space used: 172224 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