Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate Dsui_3158 Dsui_3158 Na+/H+ dicarboxylate symporter
Query= SwissProt::P24943 (421 letters) >FitnessBrowser__PS:Dsui_3158 Length = 448 Score = 353 bits (907), Expect = e-102 Identities = 163/403 (40%), Positives = 268/403 (66%), Gaps = 6/403 (1%) Query: 9 QIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68 Q+ + LG+ +GA F P+ ++P+GD F++LIKM++ PI+ +++VVG+A +GD+K Sbjct: 13 QVLFAIALGVALGAFF---PETGATMKPLGDAFIKLIKMMIAPIIFATVVVGIAKMGDMK 69 Query: 69 KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMKSLEKTDIQSYVDTTNEVQHH 128 ++G++G K +IYFE+++T+A+ +GL+ NI QPG G+N+ D ++ + + Sbjct: 70 EVGRVGLKALIYFEVVSTVALAIGLIVVNILQPGAGMNVDP-STLDTKAIANYAAAAHNQ 128 Query: 129 SMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMFY 188 S + +NI+P ++ ++ KG++L ++ FSV+FGL ++ +G+K KP+++ + +F Sbjct: 129 STTDFLMNIIPNSVVDAFAKGEILQVLLFSVLFGLALSRLGDKAKPLVKILDEFSHGLFG 188 Query: 189 VTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVAKLFGI 248 V IM FAP G F + T+ K+G+ SL L L+ VY T F+FVVLG +AK G Sbjct: 189 VIGMIMHFAPIGAFGAMAFTIGKYGIGSLKQLGFLMANVYITCALFVFVVLGLIAKFTGF 248 Query: 249 NIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNLDGSTL 308 ++ + +K+EL++ T+SSE+ LP++M K+EN GC K + VIPTGYSFNLDG+++ Sbjct: 249 SLLKFLAYIKEELLIVLGTSSSESALPRMMTKLENLGCHKPVVGMVIPTGYSFNLDGTSI 308 Query: 309 YQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG--IPI 366 Y +AAIFIAQ + + +++Q+++L VL++TSKG A V G F+ L ATL T+G +P+ Sbjct: 309 YLTMAAIFIAQALNVPLTLTEQLTILGVLLLTSKGAAAVTGGGFITLAATLATLGGKLPV 368 Query: 367 EGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409 EGLA + G+DR + AR N+IGN +A I++SKWE N ++ Sbjct: 369 EGLALLLGVDRFMSEARAITNLIGNGVATIVVSKWENALNTDR 411 Lambda K H 0.326 0.143 0.404 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: 456 Number of extensions: 25 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: 448 Length adjustment: 32 Effective length of query: 389 Effective length of database: 416 Effective search space: 161824 Effective search space used: 161824 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