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 GFF967 PS417_04905 amino acid ABC transporter permease
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__WCS417:GFF967 Length = 393 Score = 387 bits (994), Expect = e-112 Identities = 194/378 (51%), Positives = 261/378 (69%), Gaps = 1/378 (0%) Query: 24 DPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFS 83 DPK R+ +QI+TIV +V W++ +NT NL SGF FL AGF I Q LI ++ Sbjct: 16 DPKLRAWLFQIITIVAVVSLGWYLFNNTQTNLQHRGITSGFDFLERSAGFGIAQHLIDYT 75 Query: 84 SDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIP 143 +YAR ++G+LNTLLV G+ AT++GF+IG+ RLS NW+I KL TVYVEVFRNIP Sbjct: 76 ESDSYARVFVIGLLNTLLVTFIGVILATLLGFVIGVARLSPNWMINKLATVYVEVFRNIP 135 Query: 144 PLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVA 203 PLL I FWY V +P PR S + ++++RGL P I G +++V+AIVA Sbjct: 136 PLLQILFWYFAVFLTMPGPRNSHNFGDTFFVSSRGLNMPAAIAADGFWPFVVSIVVAIVA 195 Query: 204 SIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGS 263 +++ARWA+KR ATG PFH W +AL + +P L ++ G PL +++P FN GG Sbjct: 196 IVLMARWANKRFEATGVPFHKFWAGLALFIVIPALCALIFGAPLHWEMPKLQGFNFVGGW 255 Query: 264 VVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQAL 323 V+ PE ++L LAL+ YTA+FIAEIVR GI+ V GQ+EAA +LGL P R V++PQAL Sbjct: 256 VLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRPGPTLRKVIIPQAL 315 Query: 324 RIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTILNQSGQAIEIVCIWGIVYLSLSI 382 R+IIPPLTSQYLNL KNSSLA IG+ ++V++ GT+LNQ+GQAIE++ I VYL++SI Sbjct: 316 RVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISI 375 Query: 383 LTSLFMNWFNAKMALVER 400 SL MNW+N ++AL+ER Sbjct: 376 SISLLMNWYNKRIALIER 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: 491 Number of extensions: 17 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