Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 (characterized)
to candidate GFF2975 HP15_2919 amino acid ABC transporter, permease protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4771 (248 letters) >FitnessBrowser__Marino:GFF2975 Length = 223 Score = 117 bits (293), Expect = 2e-31 Identities = 68/233 (29%), Positives = 124/233 (53%), Gaps = 25/233 (10%) Query: 22 FDWY---------VTGLAWTIGIAIAAWIIALTLGSILGVMRTVPNRIVSGIATCYVELF 72 FDW + G+ +T+ I+ +I LG G++ + AT Y+E+F Sbjct: 7 FDWQAAIDSIPFLIKGIPYTLLISFGGLLIGFALGIFFGLLSINKKWFLRWPATAYIEIF 66 Query: 73 RNVPLLVQLFIWYFLVPDLLPADLQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRT 132 R P+LVQ+ ++ +PDL+ + +P T+ ++ + G + + E VR Sbjct: 67 RGTPILVQVLFIFYGLPDLIGGPI--------DPLTAGIAAIALNSGAY----ISEVVRG 114 Query: 133 GIQALPKGQESAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNTSVASLIGLM 192 G+Q++ KGQ A ++G Q +W+V+ PQA+R +IPPL ++ + K+TS+ S+IG+ Sbjct: 115 GVQSIDKGQTEAGLSLGLSRTQTFWSVVWPQAFRRMIPPLGNQAIVSIKDTSLFSVIGVG 174 Query: 193 ELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRVVEKKVAVPGLISV 245 EL+ Q + + FE + + ++Y + +SL +++R VE++ GL SV Sbjct: 175 ELVRQGQIYIANTFTAFEVYFVVAILYLAITLSLSIILRFVERR----GLASV 223 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: 142 Number of extensions: 5 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: 223 Length adjustment: 23 Effective length of query: 225 Effective length of database: 200 Effective search space: 45000 Effective search space used: 45000 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