Align Glutamate:Na+ symporter (characterized)
to candidate WP_041755326.1 PST_RS03540 sodium/glutamate symporter
Query= TCDB::P73275 (402 letters) >NCBI__GCF_000013785.1:WP_041755326.1 Length = 406 Score = 312 bits (799), Expect = 1e-89 Identities = 169/386 (43%), Positives = 249/386 (64%), Gaps = 6/386 (1%) Query: 14 VAILVLYIGKYLTKKIKFLQSFNIPDAVSGGVLASLFFGLIYGIFRTEVAFNFPIRDAFL 73 +AI++L+ GK L + + L+ ++IP++V GG L + +++ + EV F+ +RD L Sbjct: 16 LAIMLLFAGKSLVQHYEPLRRYSIPESVLGGFLCTSVTAVLFFMLDIEVVFDLEVRDVML 75 Query: 74 IIFFTCIGLSSKLKVLLQGGKPLLILLATAVSFLVIQNFVGVGMASLLGQALPVGLLSGS 133 + FF IGL S ++ L++GG+PLLILL A F+V+QN + +G+AS G GL+ GS Sbjct: 76 LYFFAGIGLKSDIRNLVKGGRPLLILLVLASLFIVLQNLLSMGVASGFGLDPRAGLMLGS 135 Query: 134 ISLSGGHGTAIAWSPVFYDNHGIRNASEIAIACATFGLVFGGIVGGPIAKFLIIRNKLEP 193 ISLSGG GT +AW+P+F + GI NA E+ IA T GL+ +GGPIA +LI R+ L P Sbjct: 136 ISLSGGVGTTLAWAPLFTEQLGIGNAMELGIASNTVGLIAACCIGGPIANYLIRRHALTP 195 Query: 194 DCDTKDLTIGIRRDQDNVQ--IDYNTMLHTILVIGVTIGLGYEINDLVAKLGLMLPAFVS 251 D+ DL +G+ ++ I + +L + + +T+ LG+ N L+ G+ LP+FVS Sbjct: 196 SRDS-DLEVGVPATSADISAPISHYDILWAWMWLNMTLMLGHGFNLLLLNSGITLPSFVS 254 Query: 252 CLLAGIVLTNTIPLAF---KKFPWPAETPSLALISDVSLGLFLAISLMSLQLWTLADIGG 308 CLLAGIV+ N + A + W LALISD+ LG+FL ++LM LQLW L + Sbjct: 255 CLLAGIVIRNLLQAAIGGQRIKHWSGAGQGLALISDICLGMFLVMALMGLQLWQLGGVLV 314 Query: 309 VIALILLVQFMATVLYSIAVVFPLMGRDYNAAVVCSGYSGLTLGATPTAIANMTAVTEKF 368 + L +Q T+LY++ +VF MGR+Y A+V+ +G+ G+ LG+T TAI NMTAVT+++ Sbjct: 315 FVVTALTLQITLTILYTVLLVFRCMGRNYEASVIAAGFGGIALGSTATAIVNMTAVTQRY 374 Query: 369 GAAPQAFIVVPLVGAFFIDIANAFVI 394 GAA QAFI+VPLV FFIDI NA +I Sbjct: 375 GAAHQAFIIVPLVCGFFIDIVNALII 400 Lambda K H 0.329 0.145 0.427 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: 487 Number of extensions: 27 Number of successful extensions: 4 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: 402 Length of database: 406 Length adjustment: 31 Effective length of query: 371 Effective length of database: 375 Effective search space: 139125 Effective search space used: 139125 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: 50 (23.9 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