Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate WP_057687367.1 ABB28_RS15990 alanine:cation symporter family protein
Query= TCDB::W0WFC6 (449 letters) >NCBI__GCF_001431535.1:WP_057687367.1 Length = 489 Score = 254 bits (648), Expect = 6e-72 Identities = 152/455 (33%), Positives = 237/455 (52%), Gaps = 36/455 (7%) Query: 14 VVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQALMTC 73 +VW P ++ L L GLY + +F+ L L RL+++ R+ S +SPFQAL Sbjct: 13 IVWSPYLVALCLLGGLYFSIRTRFIQLRALPEMLRLMFKHRA----SESGLSPFQALNIS 68 Query: 74 LAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNEHVG 133 L++ VG GNIAGVA AI GGPGA+FWMW A G ++ F E LA Y+++D + ++ G Sbjct: 69 LSSRVGVGNIAGVAMAIAFGGPGAIFWMWVVAFFGASSAFVESTLAQIYKQRDAQGQYRG 128 Query: 134 GPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEVSFGVPDWVTGVAT 193 GP Y ++ GLG+R W FA+ A + Q N++A AL ++ +P + V Sbjct: 129 GPAYYMEKGLGQR--WYAVIFAICTVAAAAMLAG-TQSNAIASALHEAWDLPVHASAVGV 185 Query: 194 MLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHAFTPI 253 +L+ L+I GG+RRI V + +VP M Y++ +++V+++ E IP LI AF Sbjct: 186 VLLLALIIFGGVRRIAAVTQWIVPLMATAYLLVALVVMLLSYERIPEVLSLIMRSAFGLD 245 Query: 254 AATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIGMLGTFIDT 313 A G G AI++GV RG+ SNEAG+G+ AA V+ GL+ +IDT Sbjct: 246 ATFGAMIG----VAIQWGVRRGVLSNEAGMGSGAHPAAAAEVSHPVKQGLVQAFSVYIDT 301 Query: 314 LIICSLTGLAIITSGVWT---------------------SGASGAALSSAAFEAAMPGVG 352 +++CS T I+++G++ +G A E+A+PG G Sbjct: 302 MVVCSATAFLILSTGMYNVYDPAVNGVPDQARMLLDNLPGMEAGPRFVQHAVESALPGFG 361 Query: 353 HYILSLALVVFAYTTILGWSYYGERCWEYLAGTR----AILPFRIVWTLAIPFGAMTQLD 408 ++LA++ FA+TTIL Y G+ YL + + FR+++ + A+ Sbjct: 362 KSFVALAILPFAFTTILALYYMGDTNVSYLCRDKPAAWIVNVFRVLFLALAAYSAINSAT 421 Query: 409 FAWLVADTLNALMAIPNLIALLLLSPVVFRLTREY 443 AW + D +M+ N+IA+LLL R+Y Sbjct: 422 LAWTLGDIGVGMMSWLNIIAILLLHKPALAALRDY 456 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: 547 Number of extensions: 32 Number of successful extensions: 6 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: 489 Length adjustment: 33 Effective length of query: 416 Effective length of database: 456 Effective search space: 189696 Effective search space used: 189696 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