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 BPHYT_RS21915 BPHYT_RS21915 ABC transporter permease
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__BFirm:BPHYT_RS21915 Length = 222 Score = 93.6 bits (231), Expect = 5e-24 Identities = 64/194 (32%), Positives = 105/194 (54%), Gaps = 15/194 (7%) Query: 192 AVGIALVIAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDV 251 A +AL + I I R KR+ G F T + + G PLLV + F L F + Sbjct: 27 AASLALSCVLGLLIGIGRLTPKRRIVYG--FCTAY--LTFFRGTPLLVQL---FLLFFGL 79 Query: 252 PVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPS 311 P G ++ P F+ L L Y+A++++EIVRG I+ V +GQ EAA ++G+ Sbjct: 80 PQFG--------ILLPAFVCGMLGLGLYSAAYVSEIVRGAIQSVDRGQMEAARSIGMSSG 131 Query: 312 SVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVC 371 R +++PQA+ +IPPL ++++ L KNS+L + DL+ G I++ S +++E+ Sbjct: 132 QAMRAIILPQAIVRMIPPLGNEFIALIKNSALVSLLTIDDLMHEGQKIISVSYRSLEVYL 191 Query: 372 IWGIVYLSLSILTS 385 +VYL L+ T+ Sbjct: 192 AIALVYLVLTQATN 205 Score = 42.7 bits (99), Expect = 1e-08 Identities = 31/105 (29%), Positives = 50/105 (47%), Gaps = 22/105 (20%) Query: 92 LLVGILNTLLVAVTGIFTATIIGFLIGIGRLS-RNWLIAKLCTVYVEVFRNIPPLLVIFF 150 +L G + T+ V + + ++G LIGIGRL+ + ++ CT Y+ FR P L+ +F Sbjct: 15 ILHGAVVTVEVTAASLALSCVLGLLIGIGRLTPKRRIVYGFCTAYLTFFRGTPLLVQLFL 74 Query: 151 WYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGI 195 + G LPQ F + L P F GM+ +G+ Sbjct: 75 LFFG----LPQ--------FGILL---------PAFVCGMLGLGL 98 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: 251 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 400 Length of database: 222 Length adjustment: 26 Effective length of query: 374 Effective length of database: 196 Effective search space: 73304 Effective search space used: 73304 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: 48 (23.1 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