Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate WP_043531024.1 JH15_RS12965 amino acid ABC transporter permease
Query= CharProtDB::CH_011913 (426 letters) >NCBI__GCF_000759345.1:WP_043531024.1 Length = 396 Score = 300 bits (767), Expect = 7e-86 Identities = 176/409 (43%), Positives = 245/409 (59%), Gaps = 33/409 (8%) Query: 20 DTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYS 79 D R++T QI++++ L+ ++NN NL A+G F FL AG+ + Q+LI YS Sbjct: 19 DPAKRALTFQILLMIGVAIFLLGIVNNTQDNLAARGITTGFGFLTNTAGFGIVQSLIDYS 78 Query: 80 NDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIP 139 ++ ++ R + GLLNTL+VS LG + ATI+G ++G+ RLS NWL+AR+ T Y+E FRNIP Sbjct: 79 SESSYGRTFLVGLLNTLIVSALGVLAATIIGFVVGIARLSPNWLIARLATCYIEIFRNIP 138 Query: 140 LLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFD 199 LLL I + T P ++ SM + + + RG LP P F Sbjct: 139 LLLQIFFWYFAVLRTMPSARE----------------SMSLGEVIFLNVRGLYLPEPQFL 182 Query: 200 HSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSL-LI 258 G++ + +A++A ++ + W RR QEATG R W SL LI Sbjct: 183 SGFGLIPAAF-------VIAVVASIAFALWNKRR--------QEATGKRLPAGWISLALI 227 Query: 259 LFAPISALLY-GLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGI 317 L P+ LL G+ D P ++ F+F GG ++ F AL +AL++YTA+FIAEIVR+GI Sbjct: 228 LGLPLLVLLVTGVPVTWDVPALSGFNFRGGITVIPEFLALWLALSIYTASFIAEIVRSGI 287 Query: 318 QAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDL 377 QAIS GQTEAA AL L G + LVI+PQA+RVI+PPL SQ+LNL KNSSLA A+ Y DL Sbjct: 288 QAISHGQTEAAQALSLPQGLILRLVIVPQAMRVIIPPLTSQYLNLIKNSSLATAIGYPDL 347 Query: 378 RGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426 G TLNQTG+ +E + + M +YLTISL +S+ MN +N + L ER Sbjct: 348 VSVFAGTTLNQTGQAIEVIAMTMAVYLTISLLVSTFMNWFNARVALVER 396 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: 424 Number of extensions: 18 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: 426 Length of database: 396 Length adjustment: 31 Effective length of query: 395 Effective length of database: 365 Effective search space: 144175 Effective search space used: 144175 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 Sep 24 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