Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate WP_019866698.1 METMI_RS0112815 dicarboxylate/amino acid:cation symporter
Query= CharProtDB::CH_088342 (421 letters) >NCBI__GCF_000384075.1:WP_019866698.1 Length = 442 Score = 342 bits (878), Expect = 1e-98 Identities = 166/400 (41%), Positives = 264/400 (66%), Gaps = 5/400 (1%) Query: 9 QIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68 Q+ + +GI++G P+ A ++P+GD F++LIKM++ PIV ++V G+A + ++ Sbjct: 37 QVLAAIFMGILLGHFC---PETAVAMKPLGDGFIKLIKMLIAPIVFCTVVTGIAGMQSME 93 Query: 69 KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMKSLEKTDIQSYVDTTNEVQHH 128 ++G++G K ++YFE+++T+A+V+GLL +I QPGAG+N+ + D QS T + H Sbjct: 94 RVGRVGIKLLLYFEVVSTLALVIGLLVVHIIQPGAGMNIDA-RNLDAQSLQGYTEAAKTH 152 Query: 129 SMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMFY 188 + V +NI+P ++ ++ + GD+L ++ F+V+FG +A IG+KG V++F +E +F Sbjct: 153 NTVSFLLNIIPVSVVDAFAKGDILQVLLFAVLFGCSLAVIGDKGALVMRFIHNVSEVLFG 212 Query: 189 VTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVAKLFGI 248 + IMK AP G F + T+ ++GV +L PL+KL+ Y FIF VLG +A+ G Sbjct: 213 IVETIMKLAPLGAFGAMAFTIGQYGVHALAPLAKLMGSFYLACGVFIFGVLGLIARWSGF 272 Query: 249 NIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDGSTL 308 ++ I +KDEL++ T+SSE+VLPRIM K+E+ GC K + VIPTGYSFNLDG+++ Sbjct: 273 SLVKFIIYIKDELLIVLGTSSSESVLPRIMGKLERLGCAKPVVGLVIPTGYSFNLDGTSI 332 Query: 309 YQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV-GIPVE 367 Y +AA+F+AQ ++ Q+++LL VL++TSKG AG+ G F+ L ATL TV IPV Sbjct: 333 YLTMAAVFVAQATNTPLTWGQELTLLGVLLLTSKGAAGITGSGFITLAATLSTVPTIPVA 392 Query: 368 GLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNE 407 GLA I GIDR + AR N+IGN +A ++ ++WE +E Sbjct: 393 GLALILGIDRFMSEARALTNLIGNGVATVVAARWENALDE 432 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: 432 Number of extensions: 16 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: 442 Length adjustment: 32 Effective length of query: 389 Effective length of database: 410 Effective search space: 159490 Effective search space used: 159490 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 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