Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate 8501185 DvMF_1919 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_05500 (242 letters) >FitnessBrowser__Miya:8501185 Length = 223 Score = 112 bits (281), Expect = 5e-30 Identities = 69/215 (32%), Positives = 113/215 (52%), Gaps = 10/215 (4%) Query: 21 PLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSRVKLLRIPAQLYTTLIRGVPDLVLML 80 PLL+ G +TI ++ L + LLG AK +R KL R A +Y IRG P +V ++ Sbjct: 15 PLLLGGVHLTIIITLGGLAIGFLLGTATGLAKTARGKLPRALADIYVEAIRGTPLIVQVM 74 Query: 81 LIFYSLQTWLTSFTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILAVPRGQVEA 140 +++ + + I P AG+I + GAY E RGA+ ++ GQ EA Sbjct: 75 FLYFGVPLATG----------MRIPPVTAGIIAIAVNSGAYIAEIVRGAVESIDVGQTEA 124 Query: 141 ATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQDAGKS 200 + GL R Q +VV+PQ R +P +GN +++ LK T+L+ +IG+ +L + Q+ Sbjct: 125 GRSIGLTRMQTLLYVVWPQAFRRMIPPLGNQFIISLKDTSLLVVIGVGELTRQGQEIIAV 184 Query: 201 TYQLFYFLVLAALIYLLITSASNFILRWLERRYAA 235 ++ F + A++YL++T + LR ER+ A Sbjct: 185 NFRAFEVWLTVAVMYLVMTLSIARALRVYERKLNA 219 Lambda K H 0.329 0.142 0.423 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: 119 Number of extensions: 7 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: 223 Length adjustment: 23 Effective length of query: 219 Effective length of database: 200 Effective search space: 43800 Effective search space used: 43800 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