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 PP_5023 PP_5023 Amino acid ABC transporter, permease protein
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__Putida:PP_5023 Length = 320 Score = 82.4 bits (202), Expect = 2e-20 Identities = 43/123 (34%), Positives = 75/123 (60%), Gaps = 2/123 (1%) Query: 275 ALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIPPLTSQY 334 AL+ +T +++AEIVR G++ + KGQ+EAA +LGL+ R V++PQA + ++PPL Q+ Sbjct: 196 ALALFTGAYVAEIVRAGVQSIAKGQNEAARSLGLNAGQSMRHVILPQAFKRVLPPLAGQF 255 Query: 335 LNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEI-VCIWGIVYLSLSILTSLFMNWFNA 393 ++L K++SL I ++L G + S EI C+ G+ YL +++ S + Sbjct: 256 ISLVKDTSLVSVIAITELTKSGREAITTSFSTFEIWFCVAGL-YLLINLPLSHIASRLER 314 Query: 394 KMA 396 ++A Sbjct: 315 RLA 317 Score = 49.7 bits (117), Expect = 1e-10 Identities = 30/80 (37%), Positives = 42/80 (52%) Query: 89 ARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVI 148 A L G+ TL ++V +IG G+ RLS N + L TVYVE+ R P L+ I Sbjct: 115 AGPLAWGLWTTLWISVVSGALGLVIGLFAGLCRLSNNPTLRDLSTVYVELVRGTPLLVQI 174 Query: 149 FFWYLGVLSVLPQPRESVGL 168 F +Y + +VL RE G+ Sbjct: 175 FIFYFFIGTVLNLSREFAGV 194 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: 313 Number of extensions: 17 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: 320 Length adjustment: 29 Effective length of query: 371 Effective length of database: 291 Effective search space: 107961 Effective search space used: 107961 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: 49 (23.5 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