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 AO353_04605 AO353_04605 amino acid ABC transporter permease
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04605 Length = 365 Score = 389 bits (999), Expect = e-113 Identities = 200/376 (53%), Positives = 255/376 (67%), Gaps = 15/376 (3%) Query: 11 TSILAAEPPPPGER-GAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVWS 69 T I + PPPG R G +AW+R ++ ++ + +LT+ A LI VP +++W + A W Sbjct: 3 THIFKPDMPPPGTRIGILAWMREHMFSSWINTLLTLFAFYLIYLVVPPILHWAILDANWV 62 Query: 70 GPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILLLV 129 G R C GACW FI ++ QF++G YP RWR + L ++ + Sbjct: 63 GTTRADCTK-----------EGACWVFIQQRFGQFMYGYYPPELRWRVDLTVWLAVIGVA 111 Query: 130 PMLIPSAPRKGLNAILLFAVLPVIAFWLLHGGF-GLEVVETPLWGGLMVTLVLSFVGIAV 188 P+ I PRK + + + P++A+ LLHG GL V T WGGLM+TLV++ VGI Sbjct: 112 PLFISRFPRKAVYGLSFLVLYPIVAYILLHGDILGLTNVATSQWGGLMLTLVIATVGIVG 171 Query: 189 SLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLL 248 +LP+GI+LALGRRS +P IR++CVTFIE RGVPLITVLFM+SVMLPLFLP G N DKLL Sbjct: 172 ALPLGIMLALGRRSNLPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLL 231 Query: 249 RALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSI 308 RALIGV +F SAY+AEV+RGGLQAIPKGQ+E A ++GLGYW+ L+I+PQA+KLVIP I Sbjct: 232 RALIGVILFQSAYVAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGI 291 Query: 309 VNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMS 368 VNTFI FKDTSLV IIG+FDLL VK +D W T G +FA +FW+FCFGMS Sbjct: 292 VNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPKWLGMAT--EGYVFAALVFWIFCFGMS 349 Query: 369 RYSGFMERHLDTGHKR 384 RYS +ER LDTGHKR Sbjct: 350 RYSMHLERKLDTGHKR 365 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: 576 Number of extensions: 27 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