Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 202642 SO3541 sodium:alanine symporter family protein (NCBI ptt file)
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__MR1:202642 Length = 488 Score = 276 bits (707), Expect = 8e-79 Identities = 157/443 (35%), Positives = 246/443 (55%), Gaps = 9/443 (2%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70 LN ++WG L++ ++G GLY L L F+ L +++ R + +S FQ Sbjct: 9 LNALLWGKLLVYGLVGAGLYFTLRLVFIQLTHFKHSLKIMTMSRQGCESG---LSSFQVF 65 Query: 71 MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130 T +AA VG GN+AGVA AI GPGA+FWMW A++GMAT E LA Y+ +D + Sbjct: 66 CTSMAARVGAGNMAGVAVAIGAAGPGAVFWMWLIAMLGMATAMVESTLAQVYKVRDANGQ 125 Query: 131 HVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEVSFGVPDWVTG 190 GGP Y ++ GLG+RW +G FA F +A + N VQ N++ A+E FG G Sbjct: 126 FRGGPSYYMEKGLGQRW--MGVLFAFFLIIAFGLVFNAVQANTITGAMERVFGFDPTYVG 183 Query: 191 VATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHAF 250 + +L +G VI+GG+R++ +V+E +VP M + YI+ + I+++ + E +P LI AF Sbjct: 184 IGLVLASGFVIMGGLRKVARVSEFIVPIMALAYILIAFIIVLFNLEQLPAVISLIVKSAF 243 Query: 251 TPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAG--IAQAAGTTHSAVRSGLIGMLG 308 A G V A++ G+ARG+FSNEAG+G+A A A+ + G + M+G Sbjct: 244 GWQEAAAGGVAYTVAQAMQAGIARGLFSNEAGMGSAANVAASASPNPNHPASQGFVQMMG 303 Query: 309 TFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFEAAMPGVGHYILSLALVVFAYTTI 368 F+DT++IC+ T I+ SG S G L+ A + G +++A+ +F +T+I Sbjct: 304 VFVDTIVICTATAAIILLSGDIGSSDDGIRLTINAMSNHVGDWGGAFIAVAIFLFCFTSI 363 Query: 369 LGWSYYGERCWEYLAG--TRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPNL 426 + Y E +L G T+A+ FR+ + FG++ ++ W +AD LMA N+ Sbjct: 364 IANYSYAETNVMFLTGNSTKALPLFRLCVLGMVMFGSVAKISLVWNLADVSMGLMATVNI 423 Query: 427 IALLLLSPVVFRLTREYFAKARS 449 +ALLLLS + R+ +Y + +S Sbjct: 424 VALLLLSGLAIRVINDYCDQLKS 446 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: 504 Number of extensions: 25 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: 488 Length adjustment: 33 Effective length of query: 416 Effective length of database: 455 Effective search space: 189280 Effective search space used: 189280 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