Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate GFF967 PS417_04905 amino acid ABC transporter permease
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__WCS417:GFF967 Length = 393 Score = 303 bits (775), Expect = 8e-87 Identities = 177/409 (43%), Positives = 249/409 (60%), Gaps = 33/409 (8%) Query: 20 DTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYS 79 D + R+ QI+ ++ ++ +L NN NL+ +G F FL AG+ +AQ LI Y+ Sbjct: 16 DPKLRAWLFQIITIVAVVSLGWYLFNNTQTNLQHRGITSGFDFLERSAGFGIAQHLIDYT 75 Query: 80 NDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIP 139 D++ R + GLLNTLLV+ +G ILAT+LG +IGV RLS NW++ ++ TVYVE FRNIP Sbjct: 76 ESDSYARVFVIGLLNTLLVTFIGVILATLLGFVIGVARLSPNWMINKLATVYVEVFRNIP 135 Query: 140 LLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFD 199 LL IL + T P P++ S F D+ V++RG N+PA Sbjct: 136 PLLQILFWYFAVFLTMPGPRN----------------SHNFGDTFFVSSRGLNMPAAI-- 177 Query: 200 HSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWP--SLL 257 D W VS+ +AI+A++ + W +RF EATG +W +L Sbjct: 178 ----AADGFWPFVVSI-VVAIVAIVLMARWANKRF--------EATGVPFHKFWAGLALF 224 Query: 258 ILFAPISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGI 317 I+ + AL++G H + P++ F+F GG+ ++ AL +ALT+YTAAFIAEIVR+GI Sbjct: 225 IVIPALCALIFGAPLHWEMPKLQGFNFVGGWVLIPELLALTLALTVYTAAFIAEIVRSGI 284 Query: 318 QAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDL 377 +++S GQTEAA +LGLRPG T+ VI+PQALRVI+PPL SQ+LNL KNSSLA + Y ++ Sbjct: 285 KSVSHGQTEAARSLGLRPGPTLRKVIIPQALRVIIPPLTSQYLNLAKNSSLAAGIGYPEM 344 Query: 378 RGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426 G LNQTG+ +E + + M +YL IS++IS LMN YNK I L ER Sbjct: 345 VSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLLMNWYNKRIALIER 393 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: 392 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: 426 Length of database: 393 Length adjustment: 31 Effective length of query: 395 Effective length of database: 362 Effective search space: 142990 Effective search space used: 142990 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 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