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 AO353_04610 AO353_04610 amino acid ABC transporter permease
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04610 Length = 393 Score = 383 bits (983), Expect = e-111 Identities = 191/383 (49%), Positives = 261/383 (68%), Gaps = 1/383 (0%) Query: 19 RSAMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQS 78 R ++ DP+ R+ +QI+TIV ++ W++ +NT NL SGF FL AGF I Q Sbjct: 11 RLSLSDPRVRAWLFQIITIVAVISMGWYLFNNTQTNLQHRGITSGFSFLERSAGFGIAQH 70 Query: 79 LITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEV 138 LI ++ +YAR ++G+LNTLLV G+ ATI+GF++G+ RLS+NW+I KL TVYVE Sbjct: 71 LIDYTESDSYARVFVIGLLNTLLVTFIGVILATILGFIVGVARLSKNWIINKLATVYVET 130 Query: 139 FRNIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALV 198 FRNIPPLL I FWY V +P PR S + ++++RGL P G A I++V Sbjct: 131 FRNIPPLLQILFWYFAVFLTMPGPRNSHNFADTFFVSSRGLNMPAAQMANGFWAFVISIV 190 Query: 199 IAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFN 258 +AIVA +++ RWA+KR ATG PFH W +AL + +P L ++ G PL +++P FN Sbjct: 191 VAIVAIVLMCRWANKRFEATGVPFHKFWVGLALFLLIPALCALIFGVPLHWEMPKLQGFN 250 Query: 259 LTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVV 318 GG V+ PE ++L LAL+ YTA+FIAEIVR GI V GQ+EAA +LGL R V+ Sbjct: 251 FVGGWVLIPELLALTLALTVYTAAFIAEIVRSGINSVSHGQTEAARSLGLRNGPTLRKVI 310 Query: 319 VPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTILNQSGQAIEIVCIWGIVY 377 +PQALR+IIPPLTSQYLNL KNSSLA IG+ ++V++ GT+LNQ+GQAIE++ I VY Sbjct: 311 IPQALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVY 370 Query: 378 LSLSILTSLFMNWFNAKMALVER 400 L++SI SL MNW+N ++AL+ER Sbjct: 371 LAISISISLLMNWYNKRIALIER 393 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: 505 Number of extensions: 19 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: 393 Length adjustment: 31 Effective length of query: 369 Effective length of database: 362 Effective search space: 133578 Effective search space used: 133578 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