Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_09910 (229 letters) >NCBI__GCF_900115975.1:WP_092487756.1 Length = 234 Score = 156 bits (394), Expect = 4e-43 Identities = 94/227 (41%), Positives = 138/227 (60%), Gaps = 11/227 (4%) Query: 4 DVIIKWLPKLA-QGATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFFRG 62 DV+I+ LP L QGA +TL++ I+V G LL + G++R SR +R L AY+ FFRG Sbjct: 2 DVVIENLPVLIFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRG 61 Query: 63 TPLLVQLFLVYYGLA------QFDAVRSSALWP----YLRDPFWCATVTMTLHTAAYIAE 112 TPLLVQ+F+VY+G+ Q V S + P + F A + +L++ AY+AE Sbjct: 62 TPLLVQIFIVYFGIPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAE 121 Query: 113 ILRGAIQAIPKGEIEAARALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALAST 172 I R +Q+I +G++EAAR+LGM+ +A+ Y++LP+A + +P NE I MLK ++L S Sbjct: 122 IFRAGVQSIERGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSV 181 Query: 173 VTLLELTGMARTIIARTYLPVEIFFAAGMFYLLMSFLLVQGFKQLER 219 + ELT + IIARTY I+ G YL+M+F L + LER Sbjct: 182 IGFAELTRNGQLIIARTYESFAIWLTVGFIYLIMTFTLSRIVDYLER 228 Lambda K H 0.331 0.141 0.434 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: 137 Number of extensions: 3 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: 229 Length of database: 234 Length adjustment: 23 Effective length of query: 206 Effective length of database: 211 Effective search space: 43466 Effective search space used: 43466 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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