Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate Pf6N2E2_5707 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5707 Length = 450 Score = 345 bits (886), Expect = 1e-99 Identities = 165/413 (39%), Positives = 272/413 (65%), Gaps = 9/413 (2%) Query: 6 LAWQIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65 L +Q+ + + +GI++G + P+ L+P GD F++LIKM++ PI+ ++V G+ + Sbjct: 11 LYFQVIVAIAIGILLGHFY---PQTGVALKPFGDGFIKLIKMVIAPIIFCTVVSGIGGMQ 67 Query: 66 DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAG--VNMKSLEKTDIQSYVDTTN 123 ++K +GK GG ++YFEI++TIA+++GL+ NI QPG G +++ +L+ + I +++ + Sbjct: 68 NMKSVGKTGGYALLYFEIVSTIALLIGLVVVNIVQPGVGMHIDVSTLDTSKIAGFINASK 127 Query: 124 EVQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTA 183 + S++ +N++P I + + GD+L ++ FSV+FG + +G GKPVL F A Sbjct: 128 D---QSIIAFILNVIPNTIVGAFANGDILQVLMFSVLFGFALHRLGAYGKPVLDFIDRFA 184 Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVA 243 MF + N IMK AP G F + T+ +GV SL+ L +L+I Y T + F+ VLG + Sbjct: 185 HVMFIIINMIMKLAPIGAFGAMAFTIGAYGVGSLVQLGQLMICFYITCVVFVLVVLGAIC 244 Query: 244 KLFGINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNL 303 + G ++ +I+ +++EL++ T+SSE+ LPR++ KME+ G K++ VIPTGYSFNL Sbjct: 245 RAHGFSVVKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNL 304 Query: 304 DGSTLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG 363 DG+++Y +AA+FIAQ M ++ QI+LLLVL+++SKG AGV G F+VL ATL VG Sbjct: 305 DGTSIYLTMAAVFIAQATDTPMDLTHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVG 364 Query: 364 -IPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEKGKQYLA 415 +PV GLA I GIDR + AR N++GN++A I+++KW + +E++ + LA Sbjct: 365 TLPVAGLALILGIDRFMSEARALTNLVGNAVATIVVAKWVKELDEDQLQTELA 417 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: 378 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: 450 Length adjustment: 32 Effective length of query: 389 Effective length of database: 418 Effective search space: 162602 Effective search space used: 162602 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