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 GFF3102 Psest_3161 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__psRCH2:GFF3102 Length = 365 Score = 385 bits (990), Expect = e-112 Identities = 197/367 (53%), Positives = 251/367 (68%), Gaps = 14/367 (3%) Query: 18 PPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVWSGPDRTFCA 77 PPP GA+ W+R NL ++ + +LT++ L L+ VP ++ W +A W+G R C+ Sbjct: 11 PPPTISIGALGWLRANLFSSWINTLLTLVGLYLLWLIVPPVLEWAIFKADWTGETRADCS 70 Query: 78 TTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILLLVPMLIPSAP 137 GACW FI ++ QF++G YP RWR L I+ P+ + P Sbjct: 71 R-----------EGACWVFIQTRFGQFMYGFYPTELRWRVDAAAWLAIIGAAPLFLRQMP 119 Query: 138 RKGLNAILLFAVLPVIAFWLLHGGF-GLEVVETPLWGGLMVTLVLSFVGIAVSLPVGILL 196 K I V P++A+WLLHGGF GL+ V T WGGLM+T+V++ VGIA +LP+GILL Sbjct: 120 HKLRYGIGYLLVYPLLAYWLLHGGFLGLQTVPTSQWGGLMLTVVIAAVGIAGALPLGILL 179 Query: 197 ALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLRALIGVSI 256 ALGRRS MP IR+LCVTFIE RGVPLITVLFM+SVMLPLFLP G N+DKLLRA++ V Sbjct: 180 ALGRRSDMPAIRVLCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNLDKLLRAMLMVVF 239 Query: 257 FTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTF 316 F +AY+AEV+RGGLQAIPKGQ+E A ++GLGYW+ T L+I+PQA+KLVIP IVNTFI F Sbjct: 240 FEAAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSTLLVILPQALKLVIPGIVNTFIALF 299 Query: 317 KDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYSGFMER 376 KDTSLV IIG+FD L +K +D W T G +FA ++W+FCFGMSRYS +ER Sbjct: 300 KDTSLVIIIGLFDFLNSIKRATADPAWLGMST--EGYVFAALVYWMFCFGMSRYSMRLER 357 Query: 377 HLDTGHK 383 LDTGHK Sbjct: 358 KLDTGHK 364 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: 577 Number of extensions: 28 Number of successful extensions: 5 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: 365 Length adjustment: 30 Effective length of query: 354 Effective length of database: 335 Effective search space: 118590 Effective search space used: 118590 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