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 RR42_RS16450 RR42_RS16450 hypothetical protein
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS16450 Length = 211 Score = 89.0 bits (219), Expect = 1e-22 Identities = 45/113 (39%), Positives = 76/113 (67%) Query: 274 LALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIPPLTSQ 333 +ALS +A++ AEI+R GIR V +GQ EAA A+G+ + R V++PQA RI++PP Sbjct: 93 IALSMSSAAYNAEIIRAGIRAVHRGQREAAQAVGMTNPRILRHVILPQATRIVLPPYMGN 152 Query: 334 YLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSL 386 +++ TK++SLA I +L+ TI + + +A+E++ I G +YL+L+ + +L Sbjct: 153 FISHTKSTSLASVITVPELMLSAQTIYSSTYRAVEVLTIAGAIYLALTTVLTL 205 Score = 45.8 bits (107), Expect = 1e-09 Identities = 26/73 (35%), Positives = 38/73 (52%) Query: 80 ITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVF 139 I F Y LL L T+L+AV T+ G L+ +GR SR+ ++ +Y+ +F Sbjct: 3 IDFVQVLPYLPILLKAALLTILLAVVTQVCGTVFGLLLALGRDSRHAVLRGAAFIYIWIF 62 Query: 140 RNIPPLLVIFFWY 152 R P LL +FF Y Sbjct: 63 RGTPVLLHLFFVY 75 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: 185 Number of extensions: 6 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: 211 Length adjustment: 26 Effective length of query: 374 Effective length of database: 185 Effective search space: 69190 Effective search space used: 69190 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