Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate WP_110804905.1 C8J30_RS06530 amino acid ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_772 (248 letters) >NCBI__GCF_003217355.1:WP_110804905.1 Length = 262 Score = 100 bits (249), Expect = 3e-26 Identities = 66/212 (31%), Positives = 112/212 (52%), Gaps = 9/212 (4%) Query: 28 GLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWYFL 87 G+G T+ + + A+ AL+LG +L V + I +A Y E+ R VP++V L F Sbjct: 43 GIGITVFVTLFAFAGALVLGLVLAVASLSRHLIWRQLARFYTEVIRGVPIIVMLLYVAFA 102 Query: 88 VPDLLPADIQEWYKQDLNPTTSA-----FLSVVVCLGLFTTARVCEQVRTGIQALPRGQE 142 L+PA + W L P S V+ L L A + E R G+ ++ RGQ Sbjct: 103 ---LVPAVVAGWNALGL-PEASVRDFPLLARAVLALILAYAAFLAEVFRAGLLSVERGQI 158 Query: 143 AAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTA 202 AA+A+G + ++ PQA+R ++PPL ++F+ + K+SS+ S++G+ ++ K TA Sbjct: 159 EAAKALGLNGWLRFRLIIFPQAFRTVLPPLGNDFVAMVKDSSLVSVLGVADITQLGKVTA 218 Query: 203 EFSANLFEAFTLATLIYFTLNMSLMLLMRSVE 234 + FE + + LIY + ++L L +R +E Sbjct: 219 AGNFRYFETYNVVALIYLAMTVTLSLALRKLE 250 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: 146 Number of extensions: 7 Number of successful extensions: 3 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: 262 Length adjustment: 24 Effective length of query: 224 Effective length of database: 238 Effective search space: 53312 Effective search space used: 53312 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