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 AZOBR_RS15675 AZOBR_RS15675 ABC transporter permease
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__azobra:AZOBR_RS15675 Length = 224 Score = 85.9 bits (211), Expect = 1e-21 Identities = 62/198 (31%), Positives = 102/198 (51%), Gaps = 15/198 (7%) Query: 188 TGMIAVGIALVIAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPL 247 T +++G A+V+ ++ +I+ A T P W A I + F+V F + Sbjct: 24 TVQLSIG-AMVLGLIVAILCAL------GKTSGPKPVRWVINAYIEVVRNTPFLVQIFLI 76 Query: 248 TFDVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALG 307 F +P T G + P+ +L +A+ ++ EI+R GI + KGQ EA ALG Sbjct: 77 FFGLP-------TMGVRLSPDLAAL-IAMVVNVGAYATEIIRAGIESIQKGQIEAGLALG 128 Query: 308 LHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAI 367 L P V R +V+ ALR + P LTSQ++ L +SS+ AI +L +V I +Q+ ++ Sbjct: 129 LKPLQVFRYIVIKPALRTVYPALTSQFILLMLSSSVVSAISADELTSVANNIQSQTFRSF 188 Query: 368 EIVCIWGIVYLSLSILTS 385 EI + +YL L+++ S Sbjct: 189 EIYIVVTGIYLMLAMMFS 206 Score = 33.1 bits (74), Expect = 8e-06 Identities = 18/64 (28%), Positives = 32/64 (50%) Query: 92 LLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFW 151 LL G T+ +++ + I+ L +G+ S + + Y+EV RN P L+ IF Sbjct: 17 LLQGAWLTVQLSIGAMVLGLIVAILCALGKTSGPKPVRWVINAYIEVVRNTPFLVQIFLI 76 Query: 152 YLGV 155 + G+ Sbjct: 77 FFGL 80 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: 175 Number of extensions: 15 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: 224 Length adjustment: 27 Effective length of query: 373 Effective length of database: 197 Effective search space: 73481 Effective search space used: 73481 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