Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate WP_010961124.1 MCA_RS09200 dicarboxylate/amino acid:cation symporter
Query= SwissProt::P24943 (421 letters) >NCBI__GCF_000008325.1:WP_010961124.1 Length = 430 Score = 335 bits (860), Expect = 1e-96 Identities = 162/398 (40%), Positives = 266/398 (66%), Gaps = 7/398 (1%) Query: 9 QIFIGLILGIIVG-AIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDL 67 ++++ +IL +IVG A+ P++ L+P+GD F++LIKM++ PIV ++ +G+ VGDL Sbjct: 9 ELYVQVILAVIVGVALGVAWPELGVKLKPLGDGFVKLIKMMIAPIVFLTVTLGIGKVGDL 68 Query: 68 KKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNM--KSLEKTDIQSYVDTTNEV 125 +K+G +G K +IYFE +TT+A+++GL+ N+ QPG G++ K+L+ I Y T Sbjct: 69 RKIGSVGLKALIYFEALTTVALLIGLVVVNLLQPGAGIHADPKTLDAAAIGQY---TGGA 125 Query: 126 QHHSMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEA 185 + S V+ +NI+P + ++ KGD+L ++ SV+FG+ ++ GE+GKPVL + +EA Sbjct: 126 KALSGVDFVLNIIPSSAVDAFAKGDILQVLLVSVLFGVAMSRQGERGKPVLDVLERVSEA 185 Query: 186 MFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVAKL 245 F IM+ AP G F + T+ K+G ++L+ L KL+ VY T F+ +VLG VA++ Sbjct: 186 SFATIGLIMRAAPVGAFGAMAFTIGKYGPDTLLSLGKLMGGVYMTCASFVVLVLGAVARV 245 Query: 246 FGINIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNLDG 305 G +++ ++K++K+EL L T+SSE LP++MEK+E GCP++I V+PTGYSFNLDG Sbjct: 246 SGFSLWRLLKLIKEELWLVLGTSSSEAALPRLMEKLEGAGCPRSIVGLVVPTGYSFNLDG 305 Query: 306 STLYQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG-I 364 + +Y +AA+F+AQ + + Q++LL VL++TSKG A V G F+ L ATL ++ + Sbjct: 306 TAIYLTMAAVFVAQATDTPLTLGHQLTLLAVLLLTSKGAAAVTGAGFITLAATLSSLDVV 365 Query: 365 PIEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWE 402 P+ GLA + G+DR + AR N+IGN++A + +++WE Sbjct: 366 PVTGLALLLGVDRFMSEARALTNLIGNAVATLAVTRWE 403 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: 437 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: 430 Length adjustment: 32 Effective length of query: 389 Effective length of database: 398 Effective search space: 154822 Effective search space used: 154822 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