Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate WP_008510473.1 BIBO1_RS17340 sodium:alanine symporter family protein
Query= TCDB::W0WFC6 (449 letters) >NCBI__GCF_000182725.1:WP_008510473.1 Length = 477 Score = 300 bits (769), Expect = 5e-86 Identities = 174/445 (39%), Positives = 261/445 (58%), Gaps = 12/445 (2%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70 LN V W +++ +L G + + LKF+ V FR+++ +D+ ISPFQAL Sbjct: 8 LNNVFWNYILVYGLLAVGFFFTIRLKFVQFVHFPELFRVVFAAGRRDEAG---ISPFQAL 64 Query: 71 MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130 +A+ VGTGNI GVA A++LGGPGA+FWMW ALVG+AT +SE LA Y+ +++ + Sbjct: 65 TISIASRVGTGNITGVAVALYLGGPGAIFWMWIVALVGLATAYSESALAQLYKIRNQDGQ 124 Query: 131 HVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEVSFGVPDWVTG 190 + GGP + I GLG WA GA F++ L+ + N VQ N++AD++ ++F +P TG Sbjct: 125 YRGGPAFYIARGLGLPWA--GALFSVCLILSFGLVFNAVQANAIADSMVMAFNMPKLGTG 182 Query: 191 VATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHAF 250 + +++G+VI GGIR+I +VAE +VPFM YI+ ++ +L ++ +A+P LIF+ AF Sbjct: 183 IVLAILSGVVIFGGIRQIARVAEVVVPFMAFAYILMAICILAINFQAVPSTIALIFSSAF 242 Query: 251 TPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGT--THSAVRSGLIGMLG 308 A GG G + AA+ GV RG+FSNEAG+G+A A T H G + LG Sbjct: 243 GLHEAVGGVTG-GITAAMLNGVKRGLFSNEAGMGSAPNIAAVATPAPHHPSSQGFVQSLG 301 Query: 309 TFIDTLIICSLTGLAIITSGVWT--SGASGAALSSAAFEAAMPGVGHYILSLALVVFAYT 366 FIDT+++C+ T + I+ SG+ SG +G L+ A + VG Y ++ A+ FA+T Sbjct: 302 VFIDTILVCTATAIMILLSGILEPGSGLTGTQLTQMAMTHHIGDVGVYFIAAAIFFFAFT 361 Query: 367 TILGWSYYGERCWEY--LAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIP 424 +I+G Y E + L G I R + +GA + + AD LMA Sbjct: 362 SIIGNYSYAESAMTFLGLGGKVPITILRCALLAMVVWGAYESIHTVFDAADASMGLMATI 421 Query: 425 NLIALLLLSPVVFRLTREYFAKARS 449 NLIA++LLS V +LT +YFA+ R+ Sbjct: 422 NLIAIVLLSGTVKKLTVDYFAQRRA 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: 558 Number of extensions: 37 Number of successful extensions: 7 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: 477 Length adjustment: 33 Effective length of query: 416 Effective length of database: 444 Effective search space: 184704 Effective search space used: 184704 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