Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate WP_110806878.1 C8J30_RS16140 ABC transporter permease subunit
Query= reanno::Smeli:SMc02120 (384 letters) >NCBI__GCF_003217355.1:WP_110806878.1 Length = 235 Score = 103 bits (257), Expect = 5e-27 Identities = 73/236 (30%), Positives = 115/236 (48%), Gaps = 21/236 (8%) Query: 159 PGGWFGLTYVETPLWGGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEV 218 P GW L G+ VTL L+ + V L LG ++A S PV++ + + V Sbjct: 9 PQGW------GDELLAGVWVTLRLAAATLPVGLLLGFVVAAASLSRRPVLRAMGWGYTTV 62 Query: 219 IRGVPLITVLFMA--------SVMLPLFLPQ--GVTFDKFLRALIGVSLFASAYMAEVVR 268 +RG+P I LF+ + +L F PQ V F F +I ++L +A+ AEV+R Sbjct: 63 MRGMPEILTLFIVYNGLGLGLNRLLDHFAPQIGAVDFPPFAAGVIALALVFAAFAAEVLR 122 Query: 269 GGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGM 328 G QA+P+GQ ++G++ Q I LPQ + +PG+ N ++ L KDT+LVS+I + Sbjct: 123 GAFQAVPEGQVLAGLAIGMTGRQVFWRIKLPQLWRFALPGMGNLWLNLLKDTALVSVIAL 182 Query: 329 FDLLGIVRLNFSDTNWATAVTPLTGLIFAGFVFWLFCFGMSRYSGFMERLLDRSQR 384 DL+ ++ T P T + A ++W C G +E +R R Sbjct: 183 DDLMRATKVAVGVTK-----QPFTFYLAACLIYWGLCLGSELVLTRLEARANRGVR 233 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: 265 Number of extensions: 15 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: 235 Length adjustment: 27 Effective length of query: 357 Effective length of database: 208 Effective search space: 74256 Effective search space used: 74256 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 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