Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate WP_008511689.1 BIBO1_RS19985 amino acid ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_772 (248 letters) >NCBI__GCF_000182725.1:WP_008511689.1 Length = 323 Score = 112 bits (280), Expect = 9e-30 Identities = 64/207 (30%), Positives = 112/207 (54%), Gaps = 13/207 (6%) Query: 32 TIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWYFLVPDL 91 T+ I+ + IA ++ I + + N ++ G++T Y LFR +PLL+Q++I Y +P + Sbjct: 125 TLYISAISIAIATIIALIGAIAKLSQNGVIYGLSTFYTSLFRGLPLLMQIYIIYLGLPQI 184 Query: 92 LPADIQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQALPRGQEAAARAMGFK 151 + + L++ +C G + T E R GI+++P GQ+ AA A+G Sbjct: 185 ---------GYVIGAIPAGILALSLCYGAYMT----EIFRAGIESIPHGQKEAATALGLG 231 Query: 152 LPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSANLFEA 211 Q W V+LPQA RIIIPP ++F+ + K+SS+ S+IG+ EL+ + + E Sbjct: 232 SAQTMWLVILPQAMRIIIPPTGNQFIAMLKDSSLVSVIGVWELMYVARTQGQTEFRHIEM 291 Query: 212 FTLATLIYFTLNMSLMLLMRSVEKKVA 238 A++IY+ L++S + +E+ A Sbjct: 292 LITASMIYWILSISFEFIQSRIERYYA 318 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: 196 Number of extensions: 9 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: 323 Length adjustment: 26 Effective length of query: 222 Effective length of database: 297 Effective search space: 65934 Effective search space used: 65934 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 24 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