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 AZOBR_RS08665 AZOBR_RS08665 amino acid ABC transporter permease
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__azobra:AZOBR_RS08665 Length = 367 Score = 336 bits (862), Expect = 5e-97 Identities = 183/379 (48%), Positives = 237/379 (62%), Gaps = 19/379 (5%) Query: 9 VRTSILAAEPPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVW 68 V T + E PP G VAW+R NL T + +LTIL L+ A+P L++WL A Sbjct: 5 VHTGSIPDERPPANTVGPVAWLRNNLFNTWYNALLTILIAWLLFKAIPPLLDWLIFSANS 64 Query: 69 SGPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILLL 128 G C GACW F+S K +FG +P E+WRP I I+++ Sbjct: 65 FGTPPQVCRQE----------GGACWTFVSEKLRFVMFGTFPYDEQWRPLIT----IVII 110 Query: 129 VPMLIPSAPR---KGLNAILLFAVLPVIAFWLLHGGFGLEVVETPLWGGLMVTLVLSFVG 185 + +++ S R K A++ A L + + G GL VE LWGGL +TL+LS VG Sbjct: 111 IALVLASCDRRFWKPWLALVWIAGLTAVGVLMWGGVLGLTYVENTLWGGLPLTLMLSVVG 170 Query: 186 IAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVD 245 ++V+ P +LLALGRRS++P IR++ VT+IE+IRGVPLI++LFMASVM PLFLPTG N D Sbjct: 171 LSVAFPASVLLALGRRSQLPAIRVISVTYIELIRGVPLISLLFMASVMFPLFLPTGVNFD 230 Query: 246 KLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVI 305 KLLRA I +F +AYMAE IRGGLQAIPKGQ+E AD+LGL YWQ II+PQA+ + I Sbjct: 231 KLLRAQIAFIMFAAAYMAEAIRGGLQAIPKGQYEAADALGLNYWQAMGKIILPQALAISI 290 Query: 306 PSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCF 365 P +VNTFI FKDTSLV IIG++DLLG K SD W +F G I+W+FC+ Sbjct: 291 PPLVNTFISFFKDTSLVIIIGLYDLLGTAKAALSDPAWRGFYR--EAYLFIGVIYWVFCY 348 Query: 366 GMSRYSGFMERHLDTGHKR 384 MS+YS +ER L GH+R Sbjct: 349 SMSKYSQKLERDLRRGHRR 367 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: 515 Number of extensions: 28 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: 367 Length adjustment: 30 Effective length of query: 354 Effective length of database: 337 Effective search space: 119298 Effective search space used: 119298 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 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