Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate WP_008511689.1 BIBO1_RS19985 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_2959 (242 letters) >NCBI__GCF_000182725.1:WP_008511689.1 Length = 323 Score = 138 bits (348), Expect = 1e-37 Identities = 79/213 (37%), Positives = 126/213 (59%), Gaps = 11/213 (5%) Query: 22 LLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLIRGVPDLVLMLL 81 L+ QGT T+ +SA+S+ ++ ++ L+GA AKLS ++ + YT+L RG+P L+ + + Sbjct: 117 LITQGTVTTLYISAISIAIATIIALIGAIAKLSQNGVIYGLSTFYTSLFRGLPLLMQIYI 176 Query: 82 IFYSLQTWLTSLTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILSVPRGQVEAA 141 I+ L + Y+ I AG++ L YGAY TE FR I S+P GQ EAA Sbjct: 177 IYLGLP----------QIGYV-IGAIPAGILALSLCYGAYMTEIFRAGIESIPHGQKEAA 225 Query: 142 TAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQDAGKST 201 TA GL Q V+ PQ MR +P GN ++ MLK ++LVS+IG+ +L+ A+ G++ Sbjct: 226 TALGLGSAQTMWLVILPQAMRIIIPPTGNQFIAMLKDSSLVSVIGVWELMYVARTQGQTE 285 Query: 202 YQLFYFLVLAALIYLLITSASNFILRWLERRYA 234 ++ L+ A++IY +++ + FI +ER YA Sbjct: 286 FRHIEMLITASMIYWILSISFEFIQSRIERYYA 318 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: 212 Number of extensions: 11 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: 323 Length adjustment: 26 Effective length of query: 216 Effective length of database: 297 Effective search space: 64152 Effective search space used: 64152 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: 47 (22.7 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