Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized)
to candidate AO353_12325 AO353_12325 ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_16285 (248 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12325 Length = 319 Score = 127 bits (319), Expect = 3e-34 Identities = 68/211 (32%), Positives = 120/211 (56%), Gaps = 14/211 (6%) Query: 28 GLGWTIAIAIVAWIIALMLGSVLGVMRTVPNRLVSGIATCYVELFRNVPLLVQLFIWYFL 87 GL T+ +++V+ ++ L++G G+ R N + ++T Y+EL R PLLVQ+FI+YF Sbjct: 120 GLWTTLWLSLVSGVLGLLIGLATGLCRLSNNPTLRDLSTVYIELVRGTPLLVQIFIFYFF 179 Query: 88 VPDLLPQNLQDWYKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPRGQESAARA 147 + +L S + + L LFT A V E +R+G+Q++ RGQ AAR+ Sbjct: 180 IGTVL--------------NLSREFAGIAALSLFTGAYVAEIIRSGVQSIARGQNEAARS 225 Query: 148 MGFKLPQIYWNVLLPQAYRIVIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSAN 207 +G Q +V+LPQA++ V+PPL +F+++ K++S+ S+I + ELL ++ S + Sbjct: 226 LGLSAGQSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELLKSGREVITTSFS 285 Query: 208 LFEAFTLATLIYFTLNMSLMLLMRMVEKKVA 238 FE +Y +N+ L + +E+++A Sbjct: 286 PFEILFCVAGLYLLINLPLSKIASRLERRLA 316 Lambda K H 0.326 0.139 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: 198 Number of extensions: 5 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: 248 Length of database: 319 Length adjustment: 26 Effective length of query: 222 Effective length of database: 293 Effective search space: 65046 Effective search space used: 65046 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: 47 (22.7 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