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 Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 239 bits (609), Expect = 1e-67 Identities = 139/406 (34%), Positives = 220/406 (54%), Gaps = 82/406 (20%) Query: 27 VAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVWSGPDRTFCATTLQGGIQP 86 +AW+R+NL ++ + +T+L + +I V L W+ +A W+ + Sbjct: 15 IAWLRQNLFSSWLNSAITLLLVVIIVTVVGRLGLWITTEARWT--------------VLV 60 Query: 87 DGWSGACWAFISAKYDQFIFGRYPLGERWRPAI-VGILFILL------------------ 127 D W+ F GRYP E+WR + +G+L L Sbjct: 61 DNWT------------LFFVGRYPAAEQWRLWLWLGLLSPTLGLTWGCLATGSHRWQRRS 108 Query: 128 ----------LVPMLIPSAPRK-GLNAIL------------------------LFAVLPV 152 + + +P P K GL AI L+ VL + Sbjct: 109 LWGWAGLAAAIAGIPLPWFPHKLGLAAIAATVPAASWLAQRCRGQAWLRFLPTLWGVLFL 168 Query: 153 IAFWLLHGGFGLEVVETPLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCV 212 + WLL GG GL V + W GL++TL + + + SLP+GILLALGR+S +P IR L V Sbjct: 169 VGLWLLQGGLGLRPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSV 228 Query: 213 TFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQA 272 T+IE+ RG+PL+T+LF VM+PL L + W +D++LRA++G++IF SAY+AE +RGGLQA Sbjct: 229 TYIELFRGLPLVTILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQA 288 Query: 273 IPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLG 332 IP+GQFE A +LGL +Q R I++PQA+++ IP+IV F+ +DT+L++I+G+ +LLG Sbjct: 289 IPQGQFEAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLG 348 Query: 333 IVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYSGFMERHL 378 I + ++ + + +F G ++WL C+G+++ S +E+ L Sbjct: 349 ISRSILANPAYLGRYAEV--YLFLGVLYWLCCYGLAQLSRRLEQRL 392 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: 591 Number of extensions: 33 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: 2 Length of query: 384 Length of database: 396 Length adjustment: 31 Effective length of query: 353 Effective length of database: 365 Effective search space: 128845 Effective search space used: 128845 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 Apr 09 2024. 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