Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate AO356_18220 AO356_18220 amino acid ABC transporter permease
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_18220 Length = 223 Score = 111 bits (278), Expect = 2e-29 Identities = 66/202 (32%), Positives = 106/202 (52%), Gaps = 9/202 (4%) Query: 172 LWGGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMA 231 LW G+++TL L +G+ + LG +LAL R S+ +I + ++ R +PL+ V+ Sbjct: 15 LWNGMVMTLKLMAMGVVGGIILGTILALMRLSHNKLISNIAGAYVNYFRSIPLLLVITWF 74 Query: 232 SVMLPLFLP----QGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGL 287 + +P L + F ++ +F +AY E+VR G+Q+IPKGQ A +LG+ Sbjct: 75 YLAVPFVLRWITGEDTPIGAFGSCVVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQALGM 134 Query: 288 SFWQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATA 347 ++ Q M I+LPQA + + P ++ I LF+DTSLV +G+ D L R N + Sbjct: 135 NYGQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNASRANGDIIGRSNE 194 Query: 348 VTPLTGLIFAGFVFWLFCFGMS 369 LI AG V++ F S Sbjct: 195 F-----LIVAGLVYFTISFAAS 211 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: 248 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: 384 Length of database: 223 Length adjustment: 26 Effective length of query: 358 Effective length of database: 197 Effective search space: 70526 Effective search space used: 70526 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