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 SMc02119 SMc02119 general L-amino acid transport permease ABC transporter protein
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__Smeli:SMc02119 Length = 397 Score = 551 bits (1419), Expect = e-161 Identities = 269/381 (70%), Positives = 324/381 (85%) Query: 20 SAMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSL 79 S + DP+ R IFYQ +TI+IL ++W+ NT NL R+N ASG+ F+R RAGF++GQSL Sbjct: 17 SIINDPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASGYDFVRSRAGFDVGQSL 76 Query: 80 ITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVF 139 I+F+SDSTY RALLVG +NTLLVA+TGI TATIIGF++GIGRLS NW+IAKL YVEVF Sbjct: 77 ISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVF 136 Query: 140 RNIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVI 199 RNIPPLLVIFFWY GVLS+LPQ R+++ LPF ++L+NRG+AFP+PI + G +A VI Sbjct: 137 RNIPPLLVIFFWYSGVLSILPQARDALALPFDIFLSNRGVAFPRPIAEEGAEYTLLAFVI 196 Query: 200 AIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNL 259 A+ AS+ AR+A KRQ ATG+ +WT + LI+GLPL+ F+V+G P+TFD+PVAGKFNL Sbjct: 197 AVAASVFFARYARKRQLATGERLPVLWTVLGLIIGLPLVTFLVTGAPITFDIPVAGKFNL 256 Query: 260 TGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVV 319 TGGSVVGPEFMSLFLALSFYTA+FIAEIVR GIRGV KGQ+EAA ALG+ P+ TRLVVV Sbjct: 257 TGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPALTTRLVVV 316 Query: 320 PQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLS 379 PQA+RIIIPPLTSQYLNLTKNSSLA+AIG++DLVAVGGTILNQ+GQ+IEIV IW IVYLS Sbjct: 317 PQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILNQTGQSIEIVSIWLIVYLS 376 Query: 380 LSILTSLFMNWFNAKMALVER 400 LS+ TSLFMNW+NA+MALVER Sbjct: 377 LSLATSLFMNWYNARMALVER 397 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: 642 Number of extensions: 32 Number of successful extensions: 1 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: 397 Length adjustment: 31 Effective length of query: 369 Effective length of database: 366 Effective search space: 135054 Effective search space used: 135054 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 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