Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate Ga0059261_0617 Ga0059261_0617 Na+/H+-dicarboxylate symporters
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__Korea:Ga0059261_0617 Length = 445 Score = 327 bits (838), Expect = 4e-94 Identities = 164/402 (40%), Positives = 257/402 (63%), Gaps = 9/402 (2%) Query: 7 AW--QIFIGLILGIIVG-AIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVAS 63 AW Q+++ +++ I G ++ Y P A L+P+GD F++L+KMI+ P++ +LV G+A Sbjct: 17 AWYGQLYVQVLVAIAAGVSVGYFWPDAGASLKPLGDAFIKLVKMIIAPVIFLTLVTGIAG 76 Query: 64 VGDLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMK--SLEKTDIQSYVDT 121 + +LK +G++ GK YF +T+A+VVGL+ AN QPGAG+N+ SL+ ++ YV Sbjct: 77 MTELKSVGRVAGKAFAYFLFFSTLALVVGLIVANTVQPGAGMNVDPASLDTGAVKDYVAK 136 Query: 122 TNEVQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQG 181 ++ S+V + I+P + +L+ +L ++ S++FG+ ++ +GE PV + Sbjct: 137 AHD---SSIVGFLMAIIPTTLVSALTGESLLQVLLVSILFGIALSMVGEPAAPVRDLLEK 193 Query: 182 TAEAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGG 241 T +F + +M+ AP G F + T+ K+G+ESL L+ LV Y T F+ VLG Sbjct: 194 TGLVVFKLVGILMRAAPVGAFGAMAFTIGKYGIESLANLAGLVATFYLTSAIFVVVVLGV 253 Query: 242 VAKLFGINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSF 301 VAKL G +IF +I+ L+ EL+L T+SSE+ LP +MDKME+ GC K + V+PTGYSF Sbjct: 254 VAKLAGFSIFKLIRYLRAELLLVLGTSSSESALPSLMDKMERAGCAKPVVGLVVPTGYSF 313 Query: 302 NLDGSTLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGT 361 NLDG+ +Y LAA+FIAQ +D+S+ QI+LL + M++SKG AGV G F+ L ATL Sbjct: 314 NLDGTNIYMTLAALFIAQACNVDLSLGDQIALLAIAMISSKGAAGVTGAGFITLAATLSI 373 Query: 362 V-GIPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWE 402 V +PV G+A I GIDR + R+ N IGN++A I++++W+ Sbjct: 374 VPDVPVAGMALILGIDRFMSECRSLTNFIGNAVATIVVARWD 415 Lambda K H 0.326 0.143 0.402 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: 406 Number of extensions: 14 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: 421 Length of database: 445 Length adjustment: 32 Effective length of query: 389 Effective length of database: 413 Effective search space: 160657 Effective search space used: 160657 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 (21.6 bits) S2: 51 (24.3 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