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 207828 DVU2341 amino acid ABC transproter, permease protein, His/Glu/Gln/Arg/opine family
Query= TCDB::Q52813 (400 letters) >MicrobesOnline__882:207828 Length = 233 Score = 98.2 bits (243), Expect = 2e-25 Identities = 53/125 (42%), Positives = 77/125 (61%) Query: 268 EFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIII 327 EF + ++L+ YTA+FIAE +R GI +P+ Q EA+ A GL VV+PQA RII+ Sbjct: 100 EFAAGVISLTVYTAAFIAEEIRSGIFSIPRTQLEASRACGLSFMQAMSYVVLPQAFRIIV 159 Query: 328 PPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSLF 387 PPL SQ LNL KNSSL + IG +L + I + + E + ++YL +S++ SL Sbjct: 160 PPLISQALNLFKNSSLCMTIGVMELTYMARQIESYTFHGFEAFTVSTLIYLCISLMVSLL 219 Query: 388 MNWFN 392 +N +N Sbjct: 220 INLYN 224 Score = 46.6 bits (109), Expect = 7e-10 Identities = 24/69 (34%), Positives = 37/69 (53%) Query: 92 LLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFW 151 ++ G++ T ++ + A ++G LI + RLS + E FRN P L+ IFFW Sbjct: 19 IVQGVITTCQLSGLSLVLAMLLGTLIAVMRLSGVRPFVWFSVAFTEFFRNTPLLVQIFFW 78 Query: 152 YLGVLSVLP 160 Y G +VLP Sbjct: 79 YFGSDAVLP 87 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: 232 Number of extensions: 11 Number of successful extensions: 3 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: 233 Length adjustment: 27 Effective length of query: 373 Effective length of database: 206 Effective search space: 76838 Effective search space used: 76838 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