Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate CA265_RS10595 CA265_RS10595 dicarboxylate/amino acid:cation symporter
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__Pedo557:CA265_RS10595 Length = 458 Score = 309 bits (791), Expect = 1e-88 Identities = 163/386 (42%), Positives = 245/386 (63%), Gaps = 19/386 (4%) Query: 29 KVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLKKLGKLGGKTIIYFEIITTIA 88 K Y + DIFLRLIKMIV P+V ++LVVGVA VGD+K +G++GGKT+ +F ++ ++ Sbjct: 84 KKLEYFTLLSDIFLRLIKMIVAPLVFTTLVVGVAKVGDIKAVGRIGGKTLGWFLAMSLMS 143 Query: 89 IVVGLLAANIFQPGAGVNMKSLEKTDIQSYVDTTNEVQHHSMVETFVNIVPKNIFESLST 148 +V+G++ N+F+PG + + ++ V+T + S+ + ++ PK+I ES+ST Sbjct: 144 LVLGMVLVNLFEPGRHMKLSLPDQL-----VNTGIQKAAMSVKDFIAHVFPKSIAESMST 198 Query: 149 GDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMFYVTNQIMKFAPFGVFALIGVT 208 ++L I+ FS+ FG+ AAIG+ G+ V++ F A + +T +M FAP VF + Sbjct: 199 NEILQIVVFSLFFGVATAAIGDLGQIVIKAFDAIAHVILKMTGYVMNFAPLAVFGAMTAI 258 Query: 209 VSKFGVESLIPLSKLV-------IVVYATMLFFIFAVLGGVAKLFGINIFHIIKILKDEL 261 V+K G+ L + + +++A ++F F VL IF ++ +K+ Sbjct: 259 VAKQGLNVLNTYAIFIGEFYLGLAILWAVLIFLGFLVLKK-------RIFRLVNDMKEPA 311 Query: 262 ILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDGSTLYQALAAIFIAQLY 321 +LA+STASSE P+ M +E+FGC I SFV+P GYSFNLDGS +Y A++FIAQ Y Sbjct: 312 LLAFSTASSEAAYPKTMMLLERFGCKDKIVSFVLPLGYSFNLDGSMMYMTFASLFIAQAY 371 Query: 322 GIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVGIPVEGLAFIAGIDRILDM 381 GI + QQIS+LL+LM+TSKGIAGVP S VV+ T+ + IP GLA + GID +LDM Sbjct: 372 GIHLGFEQQISMLLILMLTSKGIAGVPRASLVVIAGTIASFNIPEAGLALLIGIDPLLDM 431 Query: 382 ARTAVNVIGNSLAAIIMSKWEGQYNE 407 R+A NV+GNS+A ++SKWEG+ E Sbjct: 432 GRSATNVVGNSIATAVVSKWEGELKE 457 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: 427 Number of extensions: 22 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: 421 Length of database: 458 Length adjustment: 32 Effective length of query: 389 Effective length of database: 426 Effective search space: 165714 Effective search space used: 165714 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