Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4771 (248 letters) >NCBI__GCF_900115975.1:WP_092487756.1 Length = 234 Score = 118 bits (295), Expect = 1e-31 Identities = 77/214 (35%), Positives = 115/214 (53%), Gaps = 11/214 (5%) Query: 28 GLAWTIGIAIAAWIIALTLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWYFL 87 G T+ I I + I LG I G+ R +++ +AT YV+ FR PLLVQ+FI YF Sbjct: 15 GAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFIVYFG 74 Query: 88 VPDLLPADLQEWYKQDLNPTTSA-------FLSVVVCLGLFTTARVCEQVRTGIQALPKG 140 +P LL DLQ + T A FL+ V+ L + A V E R G+Q++ +G Sbjct: 75 IPKLL-MDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSIERG 133 Query: 141 QESAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNTSVASLIGLMELLAQTKQ 200 Q AAR++G Q V+LPQA++ +IPPL +EF+ + K+TS+ S+IG EL T+ Sbjct: 134 QMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAEL---TRN 190 Query: 201 TAEFSANLFEAFTLATLIYFTLNMSLMLLMRVVE 234 A +E+F + + F + L R+V+ Sbjct: 191 GQLIIARTYESFAIWLTVGFIYLIMTFTLSRIVD 224 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: 133 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: 234 Length adjustment: 23 Effective length of query: 225 Effective length of database: 211 Effective search space: 47475 Effective search space used: 47475 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 Apr 09 2024. 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