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_086509149.1 BZY95_RS06450 amino acid ABC transporter permease
Query= TCDB::Q52814 (384 letters) >NCBI__GCF_002151265.1:WP_086509149.1 Length = 366 Score = 402 bits (1033), Expect = e-117 Identities = 202/377 (53%), Positives = 261/377 (69%), Gaps = 14/377 (3%) Query: 9 VRTSILAAEPPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVW 68 V+ ++ A P P G +AW+R NL + P + + T+L L L+ + + W FI A W Sbjct: 3 VQHKMIEARPAPGNTVGPIAWLRINLFSGPVNTVFTLLGLYLLYVLLTPTIQWAFINADW 62 Query: 69 SGPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILLL 128 G R C+ GACW F++A+ QFI+G YP E WR IV F +L+ Sbjct: 63 VGTSRDDCSR-----------EGACWVFVNARLTQFIYGLYPRTELWRVNIVFATFAVLI 111 Query: 129 VPMLIPSAPRKGLNAILLFAVLPVIAFWLLHGG-FGLEVVETPLWGGLMVTLVLSFVGIA 187 + IP P K A+ PV AF+LL+GG FGL VVET WGGLM+TL+L+ VG+ Sbjct: 112 AWLAIPRLPLKRWVALATLVAFPVFAFFLLYGGYFGLRVVETHRWGGLMLTLILAVVGMV 171 Query: 188 VSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKL 247 +LP+GILLALGRRS+MP+++ CV FIE RGVPLIT+LFMASVMLPLFLPTG +VD+L Sbjct: 172 AALPIGILLALGRRSQMPIVKSFCVVFIEFWRGVPLITILFMASVMLPLFLPTGVSVDRL 231 Query: 248 LRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPS 307 +RALIG+++F SAYMAEVIRGGLQAIP+GQ E A +LG+GYW + LI++PQA+K++IP Sbjct: 232 VRALIGITLFQSAYMAEVIRGGLQAIPRGQEEAAAALGMGYWMRMGLIVLPQALKMMIPG 291 Query: 308 IVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGM 367 IVNTFI FKDT+LV IIG+FDLLGIV+ SD+ W + G +FA F+FW+FCF M Sbjct: 292 IVNTFISLFKDTTLVMIIGLFDLLGIVQAALSDSRWLGFA--LEGYVFAAFMFWIFCFSM 349 Query: 368 SRYSGFMERHLDTGHKR 384 SRYS ++ER L TGHKR Sbjct: 350 SRYSQYLERKLHTGHKR 366 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: 571 Number of extensions: 32 Number of successful extensions: 4 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: 366 Length adjustment: 30 Effective length of query: 354 Effective length of database: 336 Effective search space: 118944 Effective search space used: 118944 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: 50 (23.9 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