Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate GFF1853 PS417_09425 C4-dicarboxylate transporter
Query= SwissProt::P24943 (421 letters) >FitnessBrowser__WCS417:GFF1853 Length = 437 Score = 345 bits (886), Expect = 1e-99 Identities = 162/405 (40%), Positives = 272/405 (67%), Gaps = 10/405 (2%) Query: 9 QIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68 Q+ I + LG+++G + P++ L+P+GD F++LIKMI+ PI+ ++V G+ S+ D+K Sbjct: 13 QVLIAIALGVLIGHQW---PQIGIDLKPLGDGFIKLIKMIIGPIIFCTVVSGITSMHDVK 69 Query: 69 KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNM--KSLEKTDIQSYVDTTNEVQ 126 ++G++GGK ++YFE+++TIA+++G+LAA++ PG G N+ K+L+ + I +V + + Sbjct: 70 QVGRVGGKALLYFEVVSTIALLIGILAAHLLHPGVGFNIDVKTLDSSAIAGFV---GQAE 126 Query: 127 HHSMVETFV-NIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEA 185 H + F+ +++P F++ +KG++LP++F SV+FG+G+ +GEKG+P++ +E Sbjct: 127 HGEGITGFLLHVIPATFFDAFSKGEILPVLFVSVLFGVGLVMVGEKGRPLVGVINQASEV 186 Query: 186 MFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVAKL 245 F + I + AP G F I T+ K+GV SL+PL KLV Y T FFI VVLG +A+ Sbjct: 187 FFRIVGIISRVAPIGAFGAIAFTIGKYGVGSLLPLLKLVGTFYVTAFFFIAVVLGSIARY 246 Query: 246 FGINIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNLDG 305 G +IF ++ +K EL++ T+SSE+ LP++++K+E+ G K + V+PTGY+FNLDG Sbjct: 247 AGFSIFKLMGYIKSELLIVLGTSSSESALPQLIQKLESLGASKGVVGIVVPTGYTFNLDG 306 Query: 306 STLYQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV-GI 364 + +Y LA +F+AQ I +P+ QQ++LL V M+TSKG V G FV L A+L V + Sbjct: 307 TNIYMTLAVLFLAQATNIHLPLEQQLTLLAVAMLTSKGAGAVVGAGFVALAASLAVVPTV 366 Query: 365 PIEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409 P+ + I G+DR + R+ N+IGN++AA++++ WEG+ + EK Sbjct: 367 PVAAMVLILGVDRFMAECRSLTNIIGNAVAALVVAAWEGELDREK 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: 426 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: 437 Length adjustment: 32 Effective length of query: 389 Effective length of database: 405 Effective search space: 157545 Effective search space used: 157545 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