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 SMc03865 SMc03865 amino-acid transport system permease ABC transporter protein
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__Smeli:SMc03865 Length = 273 Score = 85.1 bits (209), Expect = 2e-21 Identities = 69/200 (34%), Positives = 105/200 (52%), Gaps = 10/200 (5%) Query: 190 MIAVGIALVIAIVASIIIARWAH-KRQAATGQPFHTVWTAIALIVGLPLLVFVVS--GFP 246 ++ +G+AL+ A+ +++ + A + G P + IA VG P LV V + P Sbjct: 66 VLGLGVALM-ALSEHVVLRQIARFYTEVIRGVPILVLLFYIAF-VGAPALVTVANFVAAP 123 Query: 247 LTFDVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGAL 306 L F + S++ M+L + S +FIAE+ R GI+ V KGQ EAA AL Sbjct: 124 L-ISAGWIEPFVVRDVSLMWRAIMALMIGYS----AFIAEVFRAGIQSVDKGQVEAAKAL 178 Query: 307 GLHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQA 366 GL RLVV PQA+R+I+PPL + ++ + K+SSL +G +D+ +G + S + Sbjct: 179 GLSRYQRFRLVVFPQAIRVILPPLGNDFVAMVKDSSLVSVLGVADITQMGKVYASGSFRF 238 Query: 367 IEIVCIWGIVYLSLSILTSL 386 E I VYL L+I SL Sbjct: 239 FETYSIVAYVYLVLTIGLSL 258 Score = 39.3 bits (90), Expect = 1e-07 Identities = 17/59 (28%), Positives = 35/59 (59%) Query: 92 LLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFF 150 +L G+ T+ V + G AT++G + + LS + ++ ++ Y EV R +P L+++F+ Sbjct: 46 VLKGLGVTVFVTLVGFVLATVLGLGVALMALSEHVVLRQIARFYTEVIRGVPILVLLFY 104 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: 272 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 400 Length of database: 273 Length adjustment: 28 Effective length of query: 372 Effective length of database: 245 Effective search space: 91140 Effective search space used: 91140 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: 49 (23.5 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