Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease
Query= reanno::Smeli:SMc02120 (384 letters) >NCBI__GCF_000011905.1:WP_010936196.1 Length = 273 Score = 129 bits (323), Expect = 1e-34 Identities = 74/217 (34%), Positives = 125/217 (57%), Gaps = 16/217 (7%) Query: 172 LWGGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMA 231 +W G+ +T++++ V + L LG+ ALGR S +++ L T ++E++RG+PL+ L Sbjct: 56 VWVGIGITVLVAVVSYFLMLILGMFGALGRLSKNTILRGLATFYVEIVRGIPLLVQLIWW 115 Query: 232 SVMLPLFLP---QGVTFDKFLR--------ALIGVSLFASAYMAEVVRGGLQAIPKGQYE 280 P+ + QG+ F + A+ G++ AYM+E+ R G+Q+IPKGQ E Sbjct: 116 YFAFPVIIQSIGQGLNFGPMMNYQANPIVMAIWGMTFCYGAYMSEIYRAGIQSIPKGQME 175 Query: 281 GADSLGLSFWQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFS 340 A SLG+S Q M +++LPQAL++V+P + N FI L KDTSLVS + + D++ + R F+ Sbjct: 176 AARSLGMSHTQAMRYVILPQALRVVLPPMGNEFIALLKDTSLVSTVAVADMVRLGR-EFT 234 Query: 341 DTNWATAVTPLTGLIFAGFVFWLFCFGMSRYSGFMER 377 TN+ P+ G ++ + SR ++E+ Sbjct: 235 ATNF----NPIEVWTMIGLLYLILTLLSSRLINYIEK 267 Lambda K H 0.329 0.144 0.454 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: 284 Number of extensions: 16 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: 384 Length of database: 273 Length adjustment: 28 Effective length of query: 356 Effective length of database: 245 Effective search space: 87220 Effective search space used: 87220 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: 48 (23.1 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