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 Pf1N1B4_916 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_916 Length = 375 Score = 377 bits (969), Expect = e-109 Identities = 189/374 (50%), Positives = 257/374 (68%), Gaps = 1/374 (0%) Query: 28 RSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFSSDST 87 R+ +QI+T+V +VG W++ NT NL SGF FL AGF I Q LI ++ + Sbjct: 2 RAWLFQIITVVAVVGMGWYLFDNTQTNLQHRGITSGFDFLERSAGFGIAQHLIDYTESDS 61 Query: 88 YARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLV 147 YAR ++G+LNTLLV G+ ATI+GF++G+ RLS+NW+IAKL TVYVEVFRNIPPLL Sbjct: 62 YARVFVIGLLNTLLVTFIGVILATILGFIVGVARLSKNWIIAKLATVYVEVFRNIPPLLQ 121 Query: 148 IFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVASIII 207 I FWY V +P PR S + ++++RGL P + G ++V+AIVA +++ Sbjct: 122 ILFWYFAVFLTMPGPRNSHNFGDTFFVSSRGLNMPAALAADGFWPFVASIVVAIVAIVLM 181 Query: 208 ARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGSVVGP 267 +RWA KR ATG PFH W +AL + +P L ++ G PL +++P FN GG V+ P Sbjct: 182 SRWATKRFEATGVPFHKFWAGLALFLVIPALCALIFGAPLHWEMPELKGFNFVGGWVLIP 241 Query: 268 EFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIII 327 E ++L LAL+ YTA+FIAEIVR GI+ V GQ+EAA +LGL R V++PQALR+II Sbjct: 242 ELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAAHSLGLRNGPTLRKVIIPQALRVII 301 Query: 328 PPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTILNQSGQAIEIVCIWGIVYLSLSILTSL 386 PPLTSQYLNL KNSSLA IG+ ++V++ GT+LNQ+GQAIE++ I VYL++SI SL Sbjct: 302 PPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISL 361 Query: 387 FMNWFNAKMALVER 400 MNW+N ++AL+ER Sbjct: 362 LMNWYNKRIALIER 375 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: 487 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: 375 Length adjustment: 30 Effective length of query: 370 Effective length of database: 345 Effective search space: 127650 Effective search space used: 127650 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