Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate WP_013554635.1 NITSA_RS08635 amino acid ABC transporter permease
Query= CharProtDB::CH_011913 (426 letters) >NCBI__GCF_000186245.1:WP_013554635.1 Length = 384 Score = 275 bits (704), Expect = 1e-78 Identities = 160/409 (39%), Positives = 239/409 (58%), Gaps = 33/409 (8%) Query: 20 DTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYS 79 D + R I QI+ + LF+ L ++ N N+E +G F+FL AG+D+ ++ IP++ Sbjct: 7 DEKIRGILYQIIAITLFVGFLFYIAQNTAHNIEQRGIKTGFAFLHDTAGFDITESPIPFT 66 Query: 80 NDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIP 139 TH + GLLNTL+VS G + ++++G +IG+ RLS NWL+ RI Y+ETFRNIP Sbjct: 67 PASTHLKVFEVGLLNTLIVSFWGIVFSSLIGLLIGIWRLSPNWLINRIAAAYIETFRNIP 126 Query: 140 LLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFD 199 +LL IL ++ T P + S+ FF++V + NRG +P F Sbjct: 127 VLLQILFWYNVVLATLP----------------STRHSLNFFNAVFINNRGFFMPKLVFQ 170 Query: 200 HSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSLLIL 259 D W + ++ A AI+ ++ W AK QE TG + + +++L Sbjct: 171 ------DGAWMIGAAIVA-AIIGIIFVHRW--------AKKRQEETGEQFPVFLTGIILL 215 Query: 260 FA-PISA-LLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGI 317 P+ A L+ G YP++ F+F GG F ALL AL++YTA FIAE +R+GI Sbjct: 216 IGLPLLAYLIAGRPVTAVYPELHGFNFRGGKTFTPEFLALLFALSIYTATFIAEAIRSGI 275 Query: 318 QAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDL 377 +A+ +GQ EAA +LGL P + + LVILPQA+R+ +P +I+Q+LNL KNSSLA A+ Y +L Sbjct: 276 EAVPKGQKEAATSLGLSPLQQLRLVILPQAVRIAIPSIINQYLNLIKNSSLAAAIGYPEL 335 Query: 378 RGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426 G +LNQTG+ LE +L+ ML YL ISL +S ++N +N +K+KER Sbjct: 336 VTIFAGTSLNQTGQALEILLITMLTYLLISLIVSLILNWFNAKMKIKER 384 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: 361 Number of extensions: 14 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: 384 Length adjustment: 31 Effective length of query: 395 Effective length of database: 353 Effective search space: 139435 Effective search space used: 139435 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