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 HSERO_RS19340 HSERO_RS19340 amino acid ABC transporter permease
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__HerbieS:HSERO_RS19340 Length = 216 Score = 86.7 bits (213), Expect = 6e-22 Identities = 69/211 (32%), Positives = 97/211 (45%), Gaps = 24/211 (11%) Query: 195 IALVIAIVASIIIARW-----AHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTF 249 +A V VA +IA W A R A+G I ++ G+PLLV + F F Sbjct: 25 VAFVFGGVAGFVIALWRVSPNAVLRGIASGY--------IQVVQGIPLLVIL---FVAYF 73 Query: 250 DVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLH 309 + +AG F LT G F + Y A+F+ EI RG I+ VPK Q EA+ LG + Sbjct: 74 GLAIAG-FKLTPLVAAGISF-------AIYCAAFLGEIWRGCIQAVPKTQWEASECLGFN 125 Query: 310 PSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEI 369 V++PQA++I PP + + KN+SLA IGF DL G I N + Q + Sbjct: 126 RFEQLTKVILPQAVKIATPPTVGFMVQIVKNTSLASVIGFVDLSRAGQIINNSTFQPFTV 185 Query: 370 VCIWGIVYLSLSILTSLFMNWFNAKMALVER 400 ++Y L S F K+ + R Sbjct: 186 FGCVALIYFCLCFPLSALSKHFERKLNVSHR 216 Score = 40.8 bits (94), Expect = 4e-08 Identities = 21/84 (25%), Positives = 46/84 (54%), Gaps = 2/84 (2%) Query: 92 LLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFW 151 LL + T+++++ + GF+I + R+S N ++ + + Y++V + IP L+++F Sbjct: 12 LLQAAVWTVVLSLVAFVFGGVAGFVIALWRVSPNAVLRGIASGYIQVVQGIPLLVILFVA 71 Query: 152 YLG--VLSVLPQPRESVGLPFSMY 173 Y G + P + G+ F++Y Sbjct: 72 YFGLAIAGFKLTPLVAAGISFAIY 95 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: 247 Number of extensions: 14 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: 216 Length adjustment: 26 Effective length of query: 374 Effective length of database: 190 Effective search space: 71060 Effective search space used: 71060 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