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 WP_012404402.1 BPHY_RS25820 ABC transporter permease subunit
Query= TCDB::Q52813 (400 letters) >NCBI__GCF_000020045.1:WP_012404402.1 Length = 543 Score = 77.0 bits (188), Expect = 1e-18 Identities = 66/217 (30%), Positives = 108/217 (49%), Gaps = 27/217 (12%) Query: 166 VGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVASIIIARWAHKRQAATGQPFHTV 225 +GLP+ + RG+ F + G+ G +V ++A++ ++R A G +TV Sbjct: 8 LGLPYLL----RGIGFTIAVTALGL--AGGVVVGLVLAAMQLSRVGPLAALARG---YTV 58 Query: 226 WTAIALIVGLPLLVFVVSGFPLTFDVPVAG-KFNLTGGSVVGPEFMSLFLALSFYTASFI 284 + G PL++ +V + +P G K + TG + LAL+ FI Sbjct: 59 -----IFRGTPLILQLVFAYDA---LPHIGLKLSATGAAA---------LALAANEGPFI 101 Query: 285 AEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLA 344 AEI+R G+ GV +GQ A ALG+ PS + R V+ PQA+R I+P L ++ ++ KNSSLA Sbjct: 102 AEILRAGVLGVERGQLLAGQALGMTPSVLMRRVIAPQAIRAIVPALGNESVSALKNSSLA 161 Query: 345 IAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLS 381 I +L + + + I G++YL L+ Sbjct: 162 SVIAVDELTLRSTQLASSTFDFFSIFFASGLMYLILT 198 Score = 35.4 bits (80), Expect = 4e-06 Identities = 20/61 (32%), Positives = 31/61 (50%) Query: 92 LLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFW 151 LL GI T+ V G+ ++G ++ +LSR +A L Y +FR P +L + F Sbjct: 13 LLRGIGFTIAVTALGLAGGVVVGLVLAAMQLSRVGPLAALARGYTVIFRGTPLILQLVFA 72 Query: 152 Y 152 Y Sbjct: 73 Y 73 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: 479 Number of extensions: 31 Number of successful extensions: 2 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: 400 Length of database: 543 Length adjustment: 33 Effective length of query: 367 Effective length of database: 510 Effective search space: 187170 Effective search space used: 187170 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: 51 (24.3 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