Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate HSERO_RS13105 HSERO_RS13105 C4-dicarboxylate ABC transporter
Query= SwissProt::P24943 (421 letters) >FitnessBrowser__HerbieS:HSERO_RS13105 Length = 441 Score = 343 bits (881), Expect = 5e-99 Identities = 166/407 (40%), Positives = 265/407 (65%), Gaps = 9/407 (2%) Query: 6 LAWQIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65 L +Q+ + +++GI++G + P ++P+GD F++LIKMI+ P++ ++V+G+A + Sbjct: 12 LYFQVLVAIVIGILLGHFY---PSTGEAMKPLGDGFVKLIKMIIAPVIFCTVVIGIAGME 68 Query: 66 DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMK--SLEKTDIQSYVDTTN 123 D+KK+GK GG ++YFE+++T+A+++GLL N QPG G+N+ SL+ I +Y T Sbjct: 69 DMKKVGKTGGLALLYFEVVSTVALIIGLLLVNFLQPGVGMNVDPASLDTKSIAAY---TA 125 Query: 124 EVQHHSMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTA 183 + S+ + + I+P ++ ++ KGD+L ++ +V+FG + G +G V F + + Sbjct: 126 PGKMGSVTDFVLGIIPTSMVDAFAKGDVLQVLLVAVLFGFALHKFGGRGTLVFDFIEKIS 185 Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVA 243 +F V IMK AP G F + T+ K+GV SL L+KL+ Y T + FIFVVLG + Sbjct: 186 HVLFSVVGAIMKVAPIGAFGAMSFTIGKYGVGSLFSLAKLMGTFYLTCLLFIFVVLGIIT 245 Query: 244 KLFGINIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNL 303 +L G +I+ +K +K+EL++ T+SSE+VLP+++ KMEN G K + VIPTGYSFNL Sbjct: 246 RLHGFSIWKFVKYIKEELLIVLGTSSSESVLPRMLAKMENAGAKKTVVGLVIPTGYSFNL 305 Query: 304 DGSTLYQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG 363 DG+ +Y +AA+FIAQ M Q+++LL VL++TSKG AG+ G F+VL ATL VG Sbjct: 306 DGTAIYLTMAAVFIAQATNTPMTFVQELTLLGVLLLTSKGAAGITGSGFIVLAATLSAVG 365 Query: 364 -IPIEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409 +P+ GLA I GIDR + AR N IGN +A ++++KW G+ + E+ Sbjct: 366 HVPVAGLALILGIDRFMSEARALTNTIGNGVATLVVAKWSGELDSER 412 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: 435 Number of extensions: 21 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: 441 Length adjustment: 32 Effective length of query: 389 Effective length of database: 409 Effective search space: 159101 Effective search space used: 159101 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