Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate WP_011930931.1 BBTA_RS37100 amino acid ABC transporter permease
Query= TCDB::Q52814 (384 letters) >NCBI__GCF_000015165.1:WP_011930931.1 Length = 360 Score = 296 bits (759), Expect = 5e-85 Identities = 158/365 (43%), Positives = 229/365 (62%), Gaps = 15/365 (4%) Query: 12 SILAAEPPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVWSGP 71 S+ E P P + ++ R L +P + LT+ A++A A+P ++ WL + AV P Sbjct: 5 SLPLPEAPVPSQ-ASLRQAARLLFGSPLNAALTLAFGAMLAVALPPMLRWLVLDAVLFNP 63 Query: 72 DRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILLLVPM 131 D C SGACW+FI K Q +FG YP+ ERWRPA+V +L + LL Sbjct: 64 DPAACRAA----------SGACWSFIYVKSGQLLFGIYPVEERWRPALVCLLILALLGWS 113 Query: 132 LIPSAPRKGLNAILLFAVLPVIAFWLLHGGFGLEVVETPLWGGLMVTLVLSFVGIAVSLP 191 + P++ L + + A+ ++ W++ GG GLE V T WGGL VTL+L+ V I ++ P Sbjct: 114 VRPASWTPRLLGLWISALALIV--WMMGGGLGLEEVPTSAWGGLPVTLILTVVAIGIAFP 171 Query: 192 VGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLRAL 251 VGILLAL RRS MP +R+ V IE +RG+PL+++LF+AS+MLPLFLP DK +RAL Sbjct: 172 VGILLALARRSTMPAVRIAAVVTIESVRGLPLLSILFVASIMLPLFLPEALLPDKFVRAL 231 Query: 252 IGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNT 311 + ++IF +AY+AEVIRGGLQAIP+GQ+E A +LGL +W+ +I+PQAI++VIP++ NT Sbjct: 232 VALTIFAAAYLAEVIRGGLQAIPRGQYEAAAALGLPFWRTQYRVILPQAIRVVIPALANT 291 Query: 312 FIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYS 371 I K+TSLV ++G+FDL+ K +D W S +F G IF+ F +R++ Sbjct: 292 IIVMIKNTSLVLVVGLFDLISSGKAALADPAWPSPAAET--FLFIGGIFFALSFSFARFA 349 Query: 372 GFMER 376 F+ER Sbjct: 350 DFLER 354 Lambda K H 0.330 0.145 0.469 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: 480 Number of extensions: 34 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 384 Length of database: 360 Length adjustment: 30 Effective length of query: 354 Effective length of database: 330 Effective search space: 116820 Effective search space used: 116820 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 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