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_RS31740 RR42_RS31740 ABC transporter permease
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS31740 Length = 222 Score = 90.9 bits (224), Expect = 3e-23 Identities = 64/205 (31%), Positives = 112/205 (54%), Gaps = 19/205 (9%) Query: 196 ALVIAIVASII--IARWAHKRQAATGQPFHTVWTA-IALIVGLPLLVFVVSGFPLTFDVP 252 ALV+ V ++ I R +R+ G + TA + I G PLLV + F L F +P Sbjct: 29 ALVLGCVMGLLVGIGRLDPRRRVVYG-----LCTAYVTAIRGTPLLVQL---FLLFFGLP 80 Query: 253 VAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSS 312 +F+ ++ P F+ + L Y+ ++++EIVRG I+ V KGQ EAA ++G+ Sbjct: 81 ---QFD-----ILLPAFVCGVIGLGIYSGAYVSEIVRGAIQSVDKGQMEAARSIGMSSGQ 132 Query: 313 VTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCI 372 R V++PQA+ +IPPL ++++ L KNS+L + D++ G I++ S +++E+ Sbjct: 133 AMRAVILPQAIVRMIPPLGNEFIALIKNSALVSLLTIHDVMHEGQKIISVSYRSLEVYLA 192 Query: 373 WGIVYLSLSILTSLFMNWFNAKMAL 397 +VYL L+ LF+ ++ + Sbjct: 193 IALVYLLLTSAAGLFLRHMEQRLRM 217 Score = 40.8 bits (94), Expect = 4e-08 Identities = 44/150 (29%), Positives = 64/150 (42%), Gaps = 31/150 (20%) Query: 99 TLLVAVTGIFTATIIGFLIGIGRLS-RNWLIAKLCTVYVEVFRNIPPLLVIFFWYLGVLS 157 T+ V + ++G L+GIGRL R ++ LCT YV R P L+ +F + G Sbjct: 22 TVEVTACALVLGCVMGLLVGIGRLDPRRRVVYGLCTAYVTAIRGTPLLVQLFLLFFG--- 78 Query: 158 VLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGI---ALVIAIVASIIIARWAHKR 214 LPQ F + L P F G+I +GI A V IV I + + Sbjct: 79 -LPQ--------FDILL---------PAFVCGVIGLGIYSGAYVSEIVRGAIQSVDKGQM 120 Query: 215 QAA------TGQPFHTVWTAIALIVGLPLL 238 +AA +GQ V A++ +P L Sbjct: 121 EAARSIGMSSGQAMRAVILPQAIVRMIPPL 150 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: 258 Number of extensions: 15 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