Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate WP_053937456.1 WG78_RS08860 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_2959 (242 letters) >NCBI__GCF_001294205.1:WP_053937456.1 Length = 221 Score = 135 bits (340), Expect = 7e-37 Identities = 79/217 (36%), Positives = 125/217 (57%), Gaps = 11/217 (5%) Query: 16 LQGFGPLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLIRGVPD 75 LQ P L++GT T+ + +++ +L+G L A +LS +K L+ PA LY + +RG P Sbjct: 7 LQSAWPYLLKGTGYTLLFAVGAMVGGLLVGALLAVLRLSGIKALQWPAALYVSAMRGTPL 66 Query: 76 LVLMLLIFYSLQTWLTSLTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILSVPR 135 LV + +I+Y L I+ +P AG++ L GAY +ET RGAI V R Sbjct: 67 LVQIFIIYYGLPAI-----------GIQFEPITAGILALSLNTGAYVSETMRGAINGVDR 115 Query: 136 GQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQ 195 GQ EAA + G+ R Q ++V+PQ +R A+P + N+ + ++K T+LVS+I + +L+ A + Sbjct: 116 GQWEAAFSQGMGRWQTLHYIVWPQALRLAVPSLSNSLISLIKDTSLVSVIAVTELMLATK 175 Query: 196 DAGKSTYQLFYFLVLAALIYLLITSASNFILRWLERR 232 + +T+Q F V AA IY ++ + R LERR Sbjct: 176 EVISTTFQPFPLYVAAAAIYWCLSLIFEQVQRLLERR 212 Lambda K H 0.329 0.142 0.418 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: 139 Number of extensions: 6 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: 242 Length of database: 221 Length adjustment: 23 Effective length of query: 219 Effective length of database: 198 Effective search space: 43362 Effective search space used: 43362 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 24 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