Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate BWI76_RS26760 BWI76_RS26760 C4-dicarboxylate transporter DctA
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__Koxy:BWI76_RS26760 Length = 428 Score = 338 bits (867), Expect = 2e-97 Identities = 154/402 (38%), Positives = 266/402 (66%), Gaps = 5/402 (1%) Query: 9 QIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68 Q+ + +GI++G + P++ A ++P+GD F++LIKMI+ P++ ++V G+A + +K Sbjct: 12 QVLSAIAIGILLGHFY---PELGAQMKPLGDAFVKLIKMIIAPVIFCTVVTGIAGMESMK 68 Query: 69 KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMKSLEKTDIQSYVDTTNEVQHH 128 +G+ G ++YFEI++TIA+++GL+ N+ QPGAG+N+ D ++ + + Sbjct: 69 AVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPAT-LDAKAVAVYAEQAKDQ 127 Query: 129 SMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMFY 188 +V ++I+P ++ + ++G++L ++ F+V+FG + +G KG+ + + ++ +F Sbjct: 128 GIVAFLLDIIPGSVIGAFASGNILQVLMFAVLFGFALHRLGSKGQLIFNVIESFSQVIFG 187 Query: 189 VTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVAKLFGI 248 + N IM+ AP G F + T+ K+GV +L+ L +L++ Y T + F+ VLG +AK G Sbjct: 188 IINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIVCFYITCILFVVVVLGSIAKATGF 247 Query: 249 NIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDGSTL 308 +IF I+ +++EL++ T+SSE+ LPR++DKMEK GC K++ VIPTGYSFNLDG+++ Sbjct: 248 SIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGTSI 307 Query: 309 YQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG-IPVE 367 Y +AA+FIAQ M + QI+LL+VL+++SKG AGV G F+VL AT+ VG +PV Sbjct: 308 YLTMAAVFIAQATNSHMDIFHQITLLVVLLLSSKGAAGVTGSGFIVLAATISAVGHLPVA 367 Query: 368 GLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409 GLA I GIDR + AR N++GN +A I+++KW + + ++ Sbjct: 368 GLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDSQQ 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: 412 Number of extensions: 17 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