Align Glutamate:Na+ symporter (characterized)
to candidate GFF635 PGA1_c06490 sodium/glutamate symport carrier protein GltS
Query= TCDB::P73275 (402 letters) >FitnessBrowser__Phaeo:GFF635 Length = 402 Score = 337 bits (863), Expect = 5e-97 Identities = 179/391 (45%), Positives = 256/391 (65%), Gaps = 1/391 (0%) Query: 11 TIIVAILVLYIGKYLTKKIKFLQSFNIPDAVSGGVLASLFFGLIYGIFRTEVAFNFPIRD 70 ++ + V +G L +++ L+ FNIP+ VSGG+LA++ +IY + + F RD Sbjct: 12 SLTLGFAVYLLGARLNERVPVLRRFNIPEPVSGGLLAAVVVMIIYSVGGWAITFEMATRD 71 Query: 71 AFLIIFFTCIGLSSKLKVLLQGGKPLLILLATAVSFLVIQNFVGVGMASLLGQALPVGLL 130 L++FF IGL+++L L+ GG+PL++LL ++ QN +G A L G L V +L Sbjct: 72 YLLVLFFAGIGLNARLADLVAGGRPLVLLLILTFLAILAQNVIGAAGALLFGYPLQVSVL 131 Query: 131 SGSISLSGGHGTAIAWSPVFYDNHGIRNASEIAIACATFGLVFGGIVGGPIAKFLIIRNK 190 GS +L GGHGTAIAW+P G+ A+E+ +A AT GLV +VGGP+A+FLI R+ Sbjct: 132 FGSAALIGGHGTAIAWAPDVAAQTGLTGAAELGVAVATLGLVLAALVGGPVARFLINRHG 191 Query: 191 LEPDCDTKDLTIGIRRDQDNVQ-IDYNTMLHTILVIGVTIGLGYEINDLVAKLGLMLPAF 249 L P ++ T+G+ D ++V ID+ +++ +L + V I +GY + + GL LP F Sbjct: 192 LTPARPDEEPTVGLAHDAEDVPAIDHLSLMRVMLHLNVAIIIGYFSSFALDAAGLKLPLF 251 Query: 250 VSCLLAGIVLTNTIPLAFKKFPWPAETPSLALISDVSLGLFLAISLMSLQLWTLADIGGV 309 V CL+AGIVL N A TP+LALIS+ SLG FLA+SLMSLQLWTL+ +G Sbjct: 252 VPCLIAGIVLANLRMGVMPNAAPVARTPALALISEFSLGAFLAMSLMSLQLWTLSSLGLA 311 Query: 310 IALILLVQFMATVLYSIAVVFPLMGRDYNAAVVCSGYSGLTLGATPTAIANMTAVTEKFG 369 IA+I+L Q + TV + + V+FP +GR Y AAV+ +G+ G LGATPTAIANMTAVT+++G Sbjct: 312 IAVIMLAQTVFTVAFVLFVLFPFLGRGYRAAVLAAGFGGFALGATPTAIANMTAVTKRYG 371 Query: 370 AAPQAFIVVPLVGAFFIDIANAFVIQQFLNF 400 +P AF+V+PLV AFF+DIANA VIQ +NF Sbjct: 372 PSPIAFVVLPLVSAFFVDIANAIVIQAIVNF 402 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: 34 Number of successful extensions: 3 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