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 YP_001327768.1 Smed_2100 polar amino acid ABC transporter inner membrane subunit
Query= TCDB::Q52814 (384 letters) >NCBI__GCF_000017145.1:YP_001327768.1 Length = 376 Score = 158 bits (399), Expect = 3e-43 Identities = 113/374 (30%), Positives = 184/374 (49%), Gaps = 34/374 (9%) Query: 29 WIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVWSGPDRTFCATTLQGGIQPDG 88 W R NL P D++L++ + W + W A W + L GI P Sbjct: 8 WSRHNLFGKPFDILLSLTVIPGFLWLAYQVAAWTVTTARWEIIPESL--RILMIGIFPAE 65 Query: 89 WSGACWA---FISAKYDQFIFGRYPLGERWRPAIVGILFILLLVPMLIPSAPRKGL---- 141 + W I+A + + +R G+L +L V L S Sbjct: 66 QAWRAWVAIMIIAALLGAALGCVFAFRKRHA---AGLLLVLAAVIALTGSKDLTNALLTA 122 Query: 142 NAILLFA-------VLPVIAFWLLHGGF----GLEVVETP----LWGGLMVTLVLSFVGI 186 + I +FA ++P++ LL GF + V +P LWGGL+++++L+ V Sbjct: 123 STIAIFASGCAAISLIPLLRRALLPAGFIALIAIFAVMSPPGAGLWGGLLLSILLTLVTS 182 Query: 187 AVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDK 246 VSLPVGILLA GRRSR +R +C+ +IEV+R VPLI V++ +++P+ P + + Sbjct: 183 IVSLPVGILLAFGRRSRFSSMRWICMGYIEVMRSVPLIMVVYWIWILMPVLAPQ-FGLAD 241 Query: 247 LLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIP 306 ++R +IG ++F SAY+AE +R GLQA+P+ Q E A SLG+ + R I++PQA+++ +P Sbjct: 242 VVRGMIGFTLFYSAYVAEYVRSGLQAVPREQTEAARSLGMSEFDINRSIVLPQALRVAVP 301 Query: 307 SIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFG 366 +V + F LV IIG+ D L ++ ++ + + +F L F Sbjct: 302 PLVGNVLDIFNTAPLVFIIGLTDFLRAGQMILANPQYGDRTYEVYAFLF------LTYFL 355 Query: 367 MSRYSGFMERHLDT 380 + F+ R L+T Sbjct: 356 VGSLITFVARRLET 369 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: 468 Number of extensions: 23 Number of successful extensions: 3 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: 376 Length adjustment: 30 Effective length of query: 354 Effective length of database: 346 Effective search space: 122484 Effective search space used: 122484 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