Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate AO353_12325 AO353_12325 ABC transporter permease
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12325 Length = 319 Score = 127 bits (319), Expect = 4e-34 Identities = 80/212 (37%), Positives = 118/212 (55%), Gaps = 9/212 (4%) Query: 171 PLWGGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFM 230 PL GL TL LS V + L +G+ L R SN P ++ L TV+IE++RG PL+ +F+ Sbjct: 116 PLLWGLWTTLWLSLVSGVLGLLIGLATGLCRLSNNPTLRDLSTVYIELVRGTPLLVQIFI 175 Query: 231 ASVMLPLFLPQGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFW 290 F+ + + + +SLF AY+AE++R G+Q+I +GQ E A SLGLS Sbjct: 176 ----FYFFIGTVLNLSREFAGIAALSLFTGAYVAEIIRSGVQSIARGQNEAARSLGLSAG 231 Query: 291 QKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTP 350 Q M +VLPQA K V+P + FI L KDTSLVS+I + +LL R + T+ +P Sbjct: 232 QSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELLKSGREVIT-----TSFSP 286 Query: 351 LTGLIFAGFVFWLFCFGMSRYSGFMERLLDRS 382 L ++ L +S+ + +ER L +S Sbjct: 287 FEILFCVAGLYLLINLPLSKIASRLERRLAQS 318 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: 281 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: 319 Length adjustment: 29 Effective length of query: 355 Effective length of database: 290 Effective search space: 102950 Effective search space used: 102950 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: 49 (23.5 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