Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate BPHYT_RS13585 BPHYT_RS13585 amino acid ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_772 (248 letters) >FitnessBrowser__BFirm:BPHYT_RS13585 Length = 218 Score = 120 bits (300), Expect = 3e-32 Identities = 70/216 (32%), Positives = 118/216 (54%), Gaps = 13/216 (6%) Query: 26 LSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWY 85 L G TI I +++++ +LG +L +MR NR+VS A ++ + R +P++VQLF Y Sbjct: 14 LKGAVVTIEITFCSFVLSTVLGLLLALMRVSDNRVVSNAAATFINVIRGLPIIVQLFYIY 73 Query: 86 FLVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQALPRGQEAAA 145 F++PDL SAF + + LG+ + E R GIQA+ GQ AA Sbjct: 74 FVLPDL-------------GVQLSAFQAGFIGLGIAYSVYQAENFRAGIQAIDHGQIEAA 120 Query: 146 RAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFS 205 +++G + I V+LPQA+RI +PP + + + K+SS+AS I + E+ + A + Sbjct: 121 QSIGMRGAMIMRRVVLPQAFRIALPPYGNTLVMMLKDSSLASTITVAEMTRAGQLIASST 180 Query: 206 ANLFEAFTLATLIYFTLNMSLMLLMRSVEKKVAVPG 241 FTL L+Y L++ L+ +R +E+++ + G Sbjct: 181 FQNMTVFTLVALLYLGLSLPLVYGLRRLERRLGLKG 216 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: 124 Number of extensions: 4 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: 218 Length adjustment: 23 Effective length of query: 225 Effective length of database: 195 Effective search space: 43875 Effective search space used: 43875 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: 46 (22.3 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