Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate 17589 b3528 C4-dicarboxylate transport protein (NCBI)
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__Keio:17589 Length = 428 Score = 342 bits (876), Expect = 2e-98 Identities = 158/407 (38%), Positives = 270/407 (66%), Gaps = 9/407 (2%) Query: 6 LAWQIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65 L +Q+ + +GI++G + P++ ++P+GD F++LIKMI+ P++ ++V G+A + Sbjct: 9 LYFQVLTAIAIGILLGHFY---PEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGME 65 Query: 66 DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMK--SLEKTDIQSYVDTTN 123 +K +G+ G ++YFEI++TIA+++GL+ N+ QPGAG+N+ +L+ + Y D Sbjct: 66 SMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYAD--- 122 Query: 124 EVQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTA 183 + + +V ++++P ++ + ++G++L ++ F+V+FG + +G KG+ + + + Sbjct: 123 QAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFS 182 Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVA 243 + +F + N IM+ AP G F + T+ K+GV +L+ L +L+I Y T + F+ VLG +A Sbjct: 183 QVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIA 242 Query: 244 KLFGINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNL 303 K G +IF I+ +++EL++ T+SSE+ LPR++DKMEK GC K++ VIPTGYSFNL Sbjct: 243 KATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNL 302 Query: 304 DGSTLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG 363 DG+++Y +AA+FIAQ M + QI+LL+VL+++SKG AGV G F+VL ATL VG Sbjct: 303 DGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVG 362 Query: 364 -IPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409 +PV GLA I GIDR + AR N++GN +A I+++KW + + +K Sbjct: 363 HLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKK 409 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: 405 Number of extensions: 15 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: 428 Length adjustment: 32 Effective length of query: 389 Effective length of database: 396 Effective search space: 154044 Effective search space used: 154044 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