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 PP_1298 PP_1298 putative amino acid ABC transporter - permease subunit
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__Putida:PP_1298 Length = 392 Score = 382 bits (982), Expect = e-111 Identities = 194/381 (50%), Positives = 256/381 (67%), Gaps = 1/381 (0%) Query: 21 AMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLI 80 ++ DP+ R+ +QILTIV +VG W++ HNT NL SGF FL AGF I Q LI Sbjct: 12 SLNDPRVRAWLFQILTIVFVVGLGWYLFHNTQTNLQHRGITSGFDFLDRSAGFGIAQHLI 71 Query: 81 TFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFR 140 + +YAR ++G+LNTLLV G+ ATI+GF+IG+ RLS NW+I KL TVYVE FR Sbjct: 72 PYVESDSYARVFVIGLLNTLLVTFIGVILATILGFIIGVARLSPNWMINKLATVYVETFR 131 Query: 141 NIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIA 200 NIPPLL I FWY V LP PR S+ + +++NRGL P G +AL +A Sbjct: 132 NIPPLLQILFWYFAVFLTLPGPRGSINIEDMFFISNRGLNMPGASIADGFWPFVVALALA 191 Query: 201 IVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLT 260 I A ++ R+A+KR TG PFH W + L + +P L ++ G P+T+D+P FN Sbjct: 192 IAAIALMVRYANKRFNETGVPFHKFWAGLLLFIAIPSLSVLLFGSPVTWDMPQLKGFNFV 251 Query: 261 GGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVP 320 GG V+ PE ++L LAL+ YTA+FIAEIVR GIR V GQ+EAA +LGL R V++P Sbjct: 252 GGWVLIPELLALTLALTIYTAAFIAEIVRSGIRSVSHGQTEAARSLGLREGPTLRKVIIP 311 Query: 321 QALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTILNQSGQAIEIVCIWGIVYLS 379 QALR+IIPPLTSQYLNL KNSSLA IG+ ++V++ GT+LNQ+GQAIE++ I VYL+ Sbjct: 312 QALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLA 371 Query: 380 LSILTSLFMNWFNAKMALVER 400 +SI SL MNW+N ++AL+ER Sbjct: 372 ISISISLLMNWYNKRIALIER 392 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: 496 Number of extensions: 18 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: 392 Length adjustment: 31 Effective length of query: 369 Effective length of database: 361 Effective search space: 133209 Effective search space used: 133209 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