Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate WP_086511406.1 BZY95_RS18715 sodium:alanine symporter family protein
Query= TCDB::W0WFC6 (449 letters) >NCBI__GCF_002151265.1:WP_086511406.1 Length = 468 Score = 602 bits (1553), Expect = e-177 Identities = 296/452 (65%), Positives = 362/452 (80%), Gaps = 8/452 (1%) Query: 1 MESLQKWVVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRS----- 55 ME+L +NGVVWGPLML+L+LG GLYL LGLK MP+ +LG GF+L+WQGR Sbjct: 1 METLTTIFEAINGVVWGPLMLILLLGVGLYLQLGLKLMPIRKLGTGFKLMWQGRDAKPVA 60 Query: 56 ---KDDESSGEISPFQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATK 112 K E+ GEISPF ALMT L+AT+GTGNIAGVATAI LGGPGA+FWMW TALVGMATK Sbjct: 61 GEVKKAEAEGEISPFNALMTALSATIGTGNIAGVATAIALGGPGAVFWMWITALVGMATK 120 Query: 113 FSEVVLAVHYREKDERNEHVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVN 172 F+E VLAV YRE D HVGGPM+ IKNGLG++W WLG AFA FG +A FGIGN VQ N Sbjct: 121 FAEAVLAVRYRETDSTGYHVGGPMFYIKNGLGRKWLWLGGAFAFFGAVAAFGIGNTVQSN 180 Query: 173 SMADALEVSFGVPDWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLV 232 S+ADAL+ +FG+P W+TGVA M++ G VILGGI+RI KVA LVPFM + Y+ A ++VLV Sbjct: 181 SVADALDSTFGIPHWLTGVAIMVLAGAVILGGIKRIAKVAGKLVPFMGIAYVAAGLVVLV 240 Query: 233 VHAEAIPGAFQLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAA 292 V+A + AF +IF +AF P AA GGFAGAAVMAAIRFGVARGIFSNEAGLG+A IA AA Sbjct: 241 VNAGQLGEAFGMIFYYAFNPHAAVGGFAGAAVMAAIRFGVARGIFSNEAGLGSAPIAHAA 300 Query: 293 GTTHSAVRSGLIGMLGTFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFEAAMPGVG 352 T + VR G+I MLGTFIDT+I+C++T L I+TS VW G +GA+L++ +F+AA+PG G Sbjct: 301 AKTRNPVRQGMIAMLGTFIDTIIVCTITALVILTSTVWIEGEAGASLTALSFDAALPGWG 360 Query: 353 HYILSLALVVFAYTTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWL 412 + I+SLAL VFA+TTILGWS+YGE+C+++L GTR+I+ +R+++ LAIP GAM QL F WL Sbjct: 361 NQIVSLALAVFAFTTILGWSFYGEKCFQFLFGTRSIMLYRVLFVLAIPLGAMAQLGFIWL 420 Query: 413 VADTLNALMAIPNLIALLLLSPVVFRLTREYF 444 +ADT NALMAIPNLIAL LLSPVVF++TR+YF Sbjct: 421 MADTFNALMAIPNLIALALLSPVVFKVTRDYF 452 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: 709 Number of extensions: 27 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: 468 Length adjustment: 33 Effective length of query: 416 Effective length of database: 435 Effective search space: 180960 Effective search space used: 180960 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 24 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