Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 (characterized)
to candidate PP_5023 PP_5023 Amino acid ABC transporter, permease protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4771 (248 letters) >FitnessBrowser__Putida:PP_5023 Length = 320 Score = 125 bits (314), Expect = 1e-33 Identities = 72/219 (32%), Positives = 118/219 (53%), Gaps = 18/219 (8%) Query: 24 WYVTGLAW----TIGIAIAAWIIALTLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLV 79 W LAW T+ I++ + + L +G G+ R N + ++T YVEL R PLLV Sbjct: 113 WAAGPLAWGLWTTLWISVVSGALGLVIGLFAGLCRLSNNPTLRDLSTVYVELVRGTPLLV 172 Query: 80 QLFIWYFLVPDLLPADLQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQALPK 139 Q+FI+YF + +L S + V L LFT A V E VR G+Q++ K Sbjct: 173 QIFIFYFFIGTVL--------------NLSREFAGVAALALFTGAYVAEIVRAGVQSIAK 218 Query: 140 GQESAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNTSVASLIGLMELLAQTK 199 GQ AAR++G Q +V+LPQA++ ++PPL +F+++ K+TS+ S+I + EL + Sbjct: 219 GQNEAARSLGLNAGQSMRHVILPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELTKSGR 278 Query: 200 QTAEFSANLFEAFTLATLIYFTLNMSLMLLMRVVEKKVA 238 + S + FE + +Y +N+ L + +E+++A Sbjct: 279 EAITTSFSTFEIWFCVAGLYLLINLPLSHIASRLERRLA 317 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: 175 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: 320 Length adjustment: 26 Effective length of query: 222 Effective length of database: 294 Effective search space: 65268 Effective search space used: 65268 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