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 WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit
Query= TCDB::Q52813 (400 letters) >NCBI__GCF_000016765.1:WP_012048835.1 Length = 374 Score = 210 bits (534), Expect = 6e-59 Identities = 122/366 (33%), Positives = 198/366 (54%), Gaps = 15/366 (4%) Query: 33 QILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFSSDSTYARAL 92 Q+ ++ L G V VA + N+ R + GFLR A F I +S + ++ T A A Sbjct: 16 QVALLLALAGLVLVVARTVSDNMERQDMVLSLGFLRSTAEFPIAESFLAYAPGDTIAWAF 75 Query: 93 LVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFWY 152 +VG+ N++ + + I +T+ G I + R S + L L +V++ RN+P ++ + FWY Sbjct: 76 VVGLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLVVQLLFWY 135 Query: 153 LGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVASI---IIAR 209 +L P R + ++L NRG+ + G+ + +++ ++ + +I Sbjct: 136 GVILMAFPPARAAAQPLPGLFLTNRGIT----VTTVGITGTALPMIVTVLGGLTLTLITA 191 Query: 210 WAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGSVVGPEF 269 W A+ T+ AL ++V L DVP +FN TGG + PEF Sbjct: 192 WRGHLHKASLCTLGTIVAGSAL--------WIVLDLGLARDVPHFDRFNFTGGLTLTPEF 243 Query: 270 MSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIPP 329 +++ Y ++F AEIVRGG+ GVP+GQ EA+ ALGL RLV+VPQALR+I+PP Sbjct: 244 VAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSKRQSLRLVIVPQALRMIVPP 303 Query: 330 LTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSLFMN 389 + SQ++ + KNS+LA+ +G+ DL V T +N +GQ +E V I +V+ +L+ SL MN Sbjct: 304 MNSQFITILKNSTLALVVGYPDLNFVANTAINHTGQGLEGVAILMLVFFTLASAISLAMN 363 Query: 390 WFNAKM 395 NA++ Sbjct: 364 RLNARV 369 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: 391 Number of extensions: 16 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 400 Length of database: 374 Length adjustment: 30 Effective length of query: 370 Effective length of database: 344 Effective search space: 127280 Effective search space used: 127280 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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