Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate WP_086509148.1 BZY95_RS06445 amino acid ABC transporter permease
Query= CharProtDB::CH_011913 (426 letters) >NCBI__GCF_002151265.1:WP_086509148.1 Length = 396 Score = 288 bits (738), Expect = 2e-82 Identities = 177/409 (43%), Positives = 239/409 (58%), Gaps = 33/409 (8%) Query: 20 DTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYS 79 D R++ Q++++ A L++++ N NL A+G F FL AG+ + Q+LI YS Sbjct: 19 DRAKRALLFQVLLIAAVAAFLLYIIGNTQDNLAARGITTGFGFLDRTAGFGIGQSLIEYS 78 Query: 80 NDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIP 139 + T+ R + GLLNTLLVS LG I ATI+G I+G+ RLS NWL+AR+ + Y+E FRNIP Sbjct: 79 SQSTYGRTFVVGLLNTLLVSALGVIAATIIGFIVGIARLSPNWLIARLASGYIEIFRNIP 138 Query: 140 LLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFD 199 LLL I F + AM AA + F +V RG LP P F+ Sbjct: 139 LLLQIFFWY------------FAVLRAMPAARDSYSLGEVIFLNV----RGLYLPEPLFE 182 Query: 200 HSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSL-LI 258 G++ L + +AI+A ++ W RR EATG R W SL LI Sbjct: 183 SGFGLIPLTF-------VVAIVASIALVIWNKRR--------HEATGKRLPAGWISLALI 227 Query: 259 LFAPISALLY-GLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGI 317 L P+ L+ G+ D P++ F+F GG ++ F AL +AL++YTA+FIAEIVR+GI Sbjct: 228 LGLPMLVLVATGVPVTWDVPELRGFNFRGGITIIPEFLALWLALSIYTASFIAEIVRSGI 287 Query: 318 QAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDL 377 QAI GQTEAA AL L + LV++PQALRVI+PPL SQ+LNL KNSSLA A+ Y DL Sbjct: 288 QAIPHGQTEAAQALSLPQKLVLRLVVVPQALRVIIPPLTSQYLNLIKNSSLATAIGYPDL 347 Query: 378 RGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426 G TLNQTG+ +E + + M +YL ISL +S MN +N + L ER Sbjct: 348 VSVFAGTTLNQTGQAIEVISMTMAVYLIISLLVSMFMNWFNARVALVER 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: 419 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