Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate RR42_RS31740 RR42_RS31740 ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_09905 (231 letters) >FitnessBrowser__Cup4G11:RR42_RS31740 Length = 222 Score = 128 bits (321), Expect = 1e-34 Identities = 79/217 (36%), Positives = 123/217 (56%), Gaps = 12/217 (5%) Query: 10 PALAAGALMTVKLALSALCLGLVLGLLGALAKTSPYKPLQW-LGGTYSTLVRGIPELLWV 68 P L GA +TV++ AL LG V+GLL + + P + + + L Y T +RG P L+ + Sbjct: 13 PDLVRGAGVTVEVTACALVLGCVMGLLVGIGRLDPRRRVVYGLCTAYVTAIRGTPLLVQL 72 Query: 69 LLIYFGTVNLMRALGEYLGMPDLALNAFAAGVIALGLCFGAYATEVFRGAILAIPKGHRE 128 L++FG L D+ L AF GVI LG+ GAY +E+ RGAI ++ KG E Sbjct: 73 FLLFFG-----------LPQFDILLPAFVCGVIGLGIYSGAYVSEIVRGAIQSVDKGQME 121 Query: 129 AGVALGLSKWRIFTRLIMPQMWRIALPGLGNLFMILMKDTALVSVIGLEEIMRHAQIGVT 188 A ++G+S + +I+PQ +P LGN F+ L+K++ALVS++ + ++M Q ++ Sbjct: 122 AARSIGMSSGQAMRAVILPQAIVRMIPPLGNEFIALIKNSALVSLLTIHDVMHEGQKIIS 181 Query: 189 VSKQPFTFYMVAALMYLGLTVLAMLGMHLLERRAARG 225 VS + Y+ AL+YL LT A L + +E+R G Sbjct: 182 VSYRSLEVYLAIALVYLLLTSAAGLFLRHMEQRLRMG 218 Lambda K H 0.329 0.143 0.435 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: 141 Number of extensions: 5 Number of successful extensions: 2 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: 231 Length of database: 222 Length adjustment: 22 Effective length of query: 209 Effective length of database: 200 Effective search space: 41800 Effective search space used: 41800 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 (21.8 bits) S2: 46 (22.3 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