Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate PfGW456L13_3607 Amino acid ABC transporter, permease protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_772 (248 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3607 Length = 281 Score = 109 bits (273), Expect = 5e-29 Identities = 66/220 (30%), Positives = 112/220 (50%), Gaps = 13/220 (5%) Query: 16 VGSEIYFDWYLSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNV 75 VG + D +L G T+ + + ++LLLG + + R + + G+A+ Y FR Sbjct: 65 VGLHLGPDGFLQGAALTLFLCFCSIWLSLLLGFVTALARLSRSAVAFGVASFYASFFRGT 124 Query: 76 PLLVQLFIWYFLVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQ 135 PLL+Q+ + Y +P L A + ++ L L A + E R GI Sbjct: 125 PLLIQILLIYLGLPQL-------------GVVPGAISAGIIALSLNYGAYLSEIFRAGIM 171 Query: 136 ALPRGQEAAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELL 195 A+ GQ AA A+G + +++LPQA R IIPP TS+F+++ K+SS+ S++G+ E++ Sbjct: 172 AVAPGQREAAMALGLGPVATFLHIVLPQAMRTIIPPTTSQFISMLKDSSLISVMGVWEVM 231 Query: 196 AQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRSVEK 235 + S E T A +IY+ L++ L L+ +E+ Sbjct: 232 FLAQSYGRSSYRYIEMLTTAAVIYWLLSIGLELIQNRLER 271 Lambda K H 0.326 0.140 0.433 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: 179 Number of extensions: 12 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: 281 Length adjustment: 25 Effective length of query: 223 Effective length of database: 256 Effective search space: 57088 Effective search space used: 57088 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