Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate PP_1298 PP_1298 putative amino acid ABC transporter - permease subunit
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__Putida:PP_1298 Length = 392 Score = 300 bits (768), Expect = 5e-86 Identities = 184/410 (44%), Positives = 245/410 (59%), Gaps = 35/410 (8%) Query: 20 DTRFRSITIQIVVLLLFLAGLVW-LLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPY 78 D R R+ QI+ ++ F+ GL W L +N NL+ +G F FL AG+ +AQ LIPY Sbjct: 15 DPRVRAWLFQILTIV-FVVGLGWYLFHNTQTNLQHRGITSGFDFLDRSAGFGIAQHLIPY 73 Query: 79 SNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNI 138 D++ R + GLLNTLLV+ +G ILATILG IIGV RLS NW++ ++ TVYVETFRNI Sbjct: 74 VESDSYARVFVIGLLNTLLVTFIGVILATILGFIIGVARLSPNWMINKLATVYVETFRNI 133 Query: 139 PLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAF 198 P LL IL + T P P+ S+ D ++NRG N+P + Sbjct: 134 PPLLQILFWYFAVFLTLP----------------GPRGSINIEDMFFISNRGLNMPGAS- 176 Query: 199 DHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSLLI 258 + D W V+L ALAI A+ + +RF TG +W LL+ Sbjct: 177 -----IADGFWPFVVAL-ALAIAAIALMVRYANKRF--------NETGVPFHKFWAGLLL 222 Query: 259 LFA--PISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAG 316 A +S LL+G D PQ+ F+F GG+ ++ AL +ALT+YTAAFIAEIVR+G Sbjct: 223 FIAIPSLSVLLFGSPVTWDMPQLKGFNFVGGWVLIPELLALTLALTIYTAAFIAEIVRSG 282 Query: 317 IQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMD 376 I+++S GQTEAA +LGLR G T+ VI+PQALRVI+PPL SQ+LNL KNSSLA + Y + Sbjct: 283 IRSVSHGQTEAARSLGLREGPTLRKVIIPQALRVIIPPLTSQYLNLAKNSSLAAGIGYPE 342 Query: 377 LRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426 + G LNQTG+ +E + + M +YL IS++IS LMN YNK I L ER Sbjct: 343 MVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLLMNWYNKRIALIER 392 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: 408 Number of extensions: 21 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: 392 Length adjustment: 31 Effective length of query: 395 Effective length of database: 361 Effective search space: 142595 Effective search space used: 142595 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