Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit
Query= CharProtDB::CH_011913 (426 letters) >NCBI__GCF_000016765.1:WP_012048835.1 Length = 374 Score = 174 bits (442), Expect = 3e-48 Identities = 124/394 (31%), Positives = 202/394 (51%), Gaps = 42/394 (10%) Query: 31 VVLLLFLAGLVWLLNNAYV-NLEAKGKDFNFSFLWTRAGYDLAQTLIPYSNDDTHFRALI 89 V LLL LAGLV ++ N+E + + FL + A + +A++ + Y+ DT A + Sbjct: 17 VALLLALAGLVLVVARTVSDNMERQDMVLSLGFLRSTAEFPIAESFLAYAPGDTIAWAFV 76 Query: 90 EGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPLLLWILLM-G 148 GL N++ +++L +L+T+ G I + R S + L + +V+ RN+PL++ +L G Sbjct: 77 VGLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLVVQLLFWYG 136 Query: 149 TILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFDHSLGVVDLG 208 IL P A +P ++ +TNRG + ++G+ G Sbjct: 137 VILMAFPPA-----------RAAAQPLPGLF------LTNRGITVT------TVGIT--G 171 Query: 209 WNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSLLILFAPISALLY 268 LP+ + L L + + WR + +A T + W ++ Sbjct: 172 TALPMIVTVLGGLTLTLIT--AWRGHLHKASLCTLGTIVAGSALW------------IVL 217 Query: 269 GLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQTEAA 328 LG D P +F+FTGG + F A+L +Y +AF AEIVR G+ + RGQ EA+ Sbjct: 218 DLGLARDVPHFDRFNFTGGLTLTPEFVAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEAS 277 Query: 329 YALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGITLNQ 388 ALGL +++ LVI+PQALR+IVPP+ SQF+ + KNS+LA+ V Y DL + +N Sbjct: 278 RALGLSKRQSLRLVIVPQALRMIVPPMNSQFITILKNSTLALVVGYPDL-NFVANTAINH 336 Query: 389 TGRELECMLLMMLIYLTISLTISSLMNLYNKSIK 422 TG+ LE + ++ML++ T++ IS MN N ++ Sbjct: 337 TGQGLEGVAILMLVFFTLASAISLAMNRLNARVQ 370 Lambda K H 0.326 0.139 0.419 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: 337 Number of extensions: 15 Number of successful extensions: 2 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: 426 Length of database: 374 Length adjustment: 31 Effective length of query: 395 Effective length of database: 343 Effective search space: 135485 Effective search space used: 135485 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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