Align AapQ, 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 1936976 b3269 predicted amino-acid transporter subunit (NCBI)
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__Keio:1936976 Length = 393 Score = 357 bits (916), Expect = e-103 Identities = 194/378 (51%), Positives = 250/378 (66%), Gaps = 1/378 (0%) Query: 24 DPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFS 83 +P R+ +QIL +V +VG V W+ HNT NL SGF FL AGF I Q LI + Sbjct: 16 NPTVRAWLFQILAVVAVVGIVGWLFHNTVTNLNNRGITSGFAFLDRGAGFGIVQHLIDYQ 75 Query: 84 SDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIP 143 TY R +VG+LNTLLV+ I A+++GF IG+ RLS NWL+ KL T+Y+E+FRNIP Sbjct: 76 QGDTYGRVFIVGLLNTLLVSALCIVFASVLGFFIGLARLSDNWLLRKLSTIYIEIFRNIP 135 Query: 144 PLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVA 203 PLL IFFWY VL LP PR++V +L+NRGL P P G IA +A+V+AIV Sbjct: 136 PLLQIFFWYFAVLRNLPGPRQAVSAFDLAFLSNRGLYIPSPQLGDGFIAFILAVVMAIVL 195 Query: 204 SIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGS 263 S+ + R+ Q TGQ T A LI+GLPLL + G L +DVP FN GG Sbjct: 196 SVGLFRFNKTYQIKTGQLRRTWPIAAVLIIGLPLLAQWLFGAALHWDVPALRGFNFRGGM 255 Query: 264 VVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQAL 323 V+ PE +L LALS YT++FIAEI+R GI+ VP GQ EAA +LGL R V++PQAL Sbjct: 256 VLIPELAALTLALSVYTSAFIAEIIRAGIQAVPYGQHEAARSLGLPNPVTLRQVIIPQAL 315 Query: 324 RIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTILNQSGQAIEIVCIWGIVYLSLSI 382 R+IIPPLTSQYLN+ KNSSLA AIG+ D+V++ GT+LNQ+GQAIE + + VYL +S+ Sbjct: 316 RVIIPPLTSQYLNIVKNSSLAAAIGYPDMVSLFAGTVLNQTGQAIETIAMTMSVYLIISL 375 Query: 383 LTSLFMNWFNAKMALVER 400 SL MN +N ++A+VER Sbjct: 376 TISLLMNIYNRRIAIVER 393 Lambda K H 0.327 0.141 0.432 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: 490 Number of extensions: 22 Number of successful extensions: 2 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: 400 Length of database: 393 Length adjustment: 31 Effective length of query: 369 Effective length of database: 362 Effective search space: 133578 Effective search space used: 133578 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 (21.7 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