Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate WP_086508346.1 BZY95_RS02050 ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_2959 (242 letters) >NCBI__GCF_002151265.1:WP_086508346.1 Length = 243 Score = 119 bits (297), Expect = 7e-32 Identities = 71/210 (33%), Positives = 112/210 (53%), Gaps = 2/210 (0%) Query: 26 GTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLIRGVPDLVLMLLIFYS 85 G +T +L LSL+ ++L + A + S + + +P +YT + RG P L+ + +I+Y Sbjct: 28 GLVLTTQLVFLSLVAGLVLAIPLAIGRSSGRRWISLPIYVYTYVFRGTPLLIQLYIIYYG 87 Query: 86 LQTWLTSLTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILSVPRGQVEAATAYG 145 + + + W + + F +I AY TE FRGAI + PRG++EAA AYG Sbjct: 88 V-VFFDGIQQTFLWPILR-EAFYPALIAFTLNTAAYTTEIFRGAIKATPRGEIEAARAYG 145 Query: 146 LKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQDAGKSTYQLF 205 + +G R +V P R ALP GN + ML A+A+ S++ L D+ AA+ Y F Sbjct: 146 MSQGLMMRRIVLPSAFRRALPAYGNEVIFMLHASAIASVVTLMDITGAARFVYARFYAPF 205 Query: 206 YFLVLAALIYLLITSASNFILRWLERRYAA 235 + AA IYL +T A + R+LE++ A Sbjct: 206 EAFLFAAAIYLCLTFAILYFFRYLEKKLLA 235 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: 169 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: 243 Length adjustment: 23 Effective length of query: 219 Effective length of database: 220 Effective search space: 48180 Effective search space used: 48180 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 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