Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate WP_090447274.1 BLS63_RS18550 amino acid ABC transporter permease
Query= TCDB::Q88NY3 (248 letters) >NCBI__GCF_900100495.1:WP_090447274.1 Length = 248 Score = 431 bits (1108), Expect = e-126 Identities = 210/248 (84%), Positives = 230/248 (92%) Query: 1 MNYNWDWGVFFKSTGVGSETYLDWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRL 60 MNYNWDWG+FFKSTG+GSE YL+W+ITGLGWTIAIA+ W+IALLLG+LLGV+RTVPNR Sbjct: 1 MNYNWDWGIFFKSTGIGSEIYLEWFITGLGWTIAIALAGWVIALLLGTLLGVLRTVPNRW 60 Query: 61 VSGIATAYVELFRNVPLLVQLFIWYFLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGL 120 ++G+ATAYVE+FRNVPLLVQLF+WYFLVPDLLPE L+ WFKQDL P TSA +SVV+CLGL Sbjct: 61 LAGVATAYVEIFRNVPLLVQLFLWYFLVPDLLPEPLELWFKQDLAPATSAYLSVVVCLGL 120 Query: 121 FTAARVCEQVRTGIQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVF 180 FTAARVCEQVRTGIQALPKGQ AA AMGF LPQIY VLLPQA RI+IPPLTSEFLN+F Sbjct: 121 FTAARVCEQVRTGIQALPKGQIAAGYAMGFRLPQIYREVLLPQALRIVIPPLTSEFLNIF 180 Query: 181 KNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKVAVP 240 KNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNM LM+LMR VEKKVAVP Sbjct: 181 KNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMTLMMLMRTVEKKVAVP 240 Query: 241 GLISVGGK 248 GLI+VGGK Sbjct: 241 GLIAVGGK 248 Lambda K H 0.325 0.139 0.425 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: 331 Number of extensions: 4 Number of successful extensions: 1 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: 248 Length adjustment: 24 Effective length of query: 224 Effective length of database: 224 Effective search space: 50176 Effective search space used: 50176 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 46 (22.3 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