Align Glutamate:Na+ symporter (characterized)
to candidate 3607853 Dshi_1261 sodium/glutamate symporter (RefSeq)
Query= TCDB::P73275 (402 letters) >FitnessBrowser__Dino:3607853 Length = 402 Score = 343 bits (880), Expect = 5e-99 Identities = 174/391 (44%), Positives = 265/391 (67%), Gaps = 4/391 (1%) Query: 11 TIIVAILVLYIGKYLTKKIKFLQSFNIPDAVSGGVLASLFFGLIYGIFRTEVAFNFPIRD 70 ++ + +LV +IG +LT+K++FL+ +NIP+ VSGG+ +L + + ++ F+ +RD Sbjct: 11 SVTLGLLVYFIGAFLTRKVQFLKDYNIPEPVSGGLAIALVTWAFFALTGRQIVFDLAVRD 70 Query: 71 AFLIIFFTCIGLSSKLKVLLQGGKPLLILLATAVSFLVIQNFVGVGMASLLGQALPVGLL 130 L++FF+ IGL+++L LL+GG+ LL+LL V F+V+QN VG+ L P+ +L Sbjct: 71 YLLVLFFSTIGLNARLADLLRGGRLLLVLLGLTVGFMVLQNLVGLVGTILFDLPTPMAVL 130 Query: 131 SGSISLSGGHGTAIAWSPVFYDNHGIRNASEIAIACATFGLVFGGIVGGPIAKFLIIRNK 190 GS +L GGHGTAIAW P + G A+E+ IA AT GLVF ++GGPIAK LI RN Sbjct: 131 LGSAALIGGHGTAIAWGPEIEEVTGFAAAAEVGIAAATLGLVFAALIGGPIAKRLIDRNG 190 Query: 191 LEPDCDTKDLTIGIRRDQDNVQ---IDYNTMLHTILVIGVTIGLGYEINDLVAKLGLMLP 247 L + + +G+ ++ +++ +++ ++L V I LG+ + +A G+MLP Sbjct: 191 LSGEEGAAPV-VGLEFEEPGEAPEVVNHVSLMRSMLAAHVAILLGFLAHGAIAAAGVMLP 249 Query: 248 AFVSCLLAGIVLTNTIPLAFKKFPWPAETPSLALISDVSLGLFLAISLMSLQLWTLADIG 307 FV CLL GIV +NTIP F + WPA + +LA++SD SL +FLA+SLMS+QLWTL ++G Sbjct: 250 LFVPCLLVGIVTSNTIPYLFPRLTWPAGSRALAVVSDYSLSVFLAMSLMSMQLWTLTELG 309 Query: 308 GVIALILLVQFMATVLYSIAVVFPLMGRDYNAAVVCSGYSGLTLGATPTAIANMTAVTEK 367 G + +L +Q TV + + VVF +GR++ AAV+ +G++G LGATPTAIANM++VT++ Sbjct: 310 GPLLGVLAMQVAMTVAFILLVVFAALGRNFTAAVLSAGFAGFALGATPTAIANMSSVTKR 369 Query: 368 FGAAPQAFIVVPLVGAFFIDIANAFVIQQFL 398 +G AP AFIV+PLV AFF+D+ANA +IQ F+ Sbjct: 370 YGPAPLAFIVLPLVSAFFVDLANAVIIQVFV 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: 528 Number of extensions: 33 Number of successful extensions: 2 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: 402 Length adjustment: 31 Effective length of query: 371 Effective length of database: 371 Effective search space: 137641 Effective search space used: 137641 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 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