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 Ac3H11_2554 Amino acid ABC transporter, permease protein
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2554 Length = 222 Score = 90.1 bits (222), Expect = 5e-23 Identities = 54/160 (33%), Positives = 92/160 (57%), Gaps = 11/160 (6%) Query: 229 IALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIV 288 +A I G PLLV + F L F +P G ++ P F+ + L Y+ ++++E+V Sbjct: 60 VAAIRGTPLLVQL---FILFFGLPQFG--------ILLPAFVCGVIGLGIYSGAYVSEVV 108 Query: 289 RGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIG 348 RG I+ + KGQ EAA ++G+ R VV+PQA+ +IPPL ++++ L KNS+L + Sbjct: 109 RGAIQSIDKGQMEAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLT 168 Query: 349 FSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSLFM 388 DL+ G I++ S +++E+ +VY L+ T+L + Sbjct: 169 IHDLMHEGQKIISVSYRSLEVYLAIAVVYFILTGATTLVL 208 Score = 45.8 bits (107), Expect = 1e-09 Identities = 33/105 (31%), Positives = 49/105 (46%), Gaps = 22/105 (20%) Query: 92 LLVGILNTLLVAVTGIFTATIIGFLIGIGRLS-RNWLIAKLCTVYVEVFRNIPPLLVIFF 150 LL G L T+ + + ++G L+GIGRL+ + ++ LCT YV R P L+ +F Sbjct: 15 LLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLFI 74 Query: 151 WYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGI 195 + G LPQ F + L P F G+I +GI Sbjct: 75 LFFG----LPQ--------FGILL---------PAFVCGVIGLGI 98 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: 248 Number of extensions: 12 Number of successful extensions: 3 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: 222 Length adjustment: 26 Effective length of query: 374 Effective length of database: 196 Effective search space: 73304 Effective search space used: 73304 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: 48 (23.1 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