Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 6936729 Sama_0916 sodium:alanine symporter family protein (RefSeq)
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__SB2B:6936729 Length = 480 Score = 290 bits (743), Expect = 5e-83 Identities = 165/437 (37%), Positives = 255/437 (58%), Gaps = 9/437 (2%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70 LN ++WG L++ ++G GLY + L F+ L G +++ R D G +S FQ Sbjct: 9 LNALLWGKLLVYGLVGAGLYFTVRLAFIQLTHFKHGIKVMTISRQGGD---GGLSSFQVF 65 Query: 71 MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130 T +AA VG GN+AGVA AI GPGA+FWMW A++GMAT E LA Y+ KDE + Sbjct: 66 CTSMAARVGAGNMAGVAVAIGTAGPGAVFWMWAIAVLGMATAMIESTLAQVYKVKDEDGQ 125 Query: 131 HVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEVSFGVPDWVTG 190 GGP Y ++ GLG+RW +GA F++F LA + N VQ N++ ALE FG G Sbjct: 126 FRGGPAYYMEKGLGQRW--MGALFSVFLILAFGLVFNAVQANTITGALERVFGFEPIYVG 183 Query: 191 VATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHAF 250 + ++ +G VI+GG+R++ +V+E +VPFM + Y++ + +V+VV+ + +P F LI AF Sbjct: 184 IGIVVASGFVIMGGLRKVARVSEIVVPFMALVYLLIASVVVVVNLDKLPEVFSLIIKSAF 243 Query: 251 TPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGT--THSAVRSGLIGMLG 308 A G +V A++ G+ARG+FSNEAG+G+A A+ T + G + M+G Sbjct: 244 GWQEAVAGGVAYSVAQAMQAGIARGLFSNEAGMGSAANVAASATPNPNHPASQGFVQMMG 303 Query: 309 TFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFEAAMPGVGHYILSLALVVFAYTTI 368 F+DTL+IC+ T I+ +G + + G L+ A + + G ++ A+ +F +T+I Sbjct: 304 VFVDTLVICTATAAIILLAGDMGAESDGIKLTIDALTSHVGDWGGAFIAFAIFLFCFTSI 363 Query: 369 LGWSYYGERCWEYLAGTR--AILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPNL 426 + Y E +L+G R A+ FR++ + FGAM ++ W +AD LMAI N+ Sbjct: 364 IANYSYAETNVMFLSGNRKTALPLFRLLVLGMVMFGAMAKISLVWDLADVSMGLMAIVNI 423 Query: 427 IALLLLSPVVFRLTREY 443 IAL+LLS + R+ +Y Sbjct: 424 IALVLLSGLAIRVIDDY 440 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: 516 Number of extensions: 27 Number of successful extensions: 5 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: 480 Length adjustment: 33 Effective length of query: 416 Effective length of database: 447 Effective search space: 185952 Effective search space used: 185952 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