Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS (uncharacterized)
to candidate WP_093393289.1 BM091_RS02745 asparagine--tRNA ligase
Query= curated2:Q8TXG4 (431 letters) >NCBI__GCF_900114975.1:WP_093393289.1 Length = 454 Score = 228 bits (581), Expect = 3e-64 Identities = 152/435 (34%), Positives = 221/435 (50%), Gaps = 27/435 (6%) Query: 13 ERDGEEVRLAGWVHEVRDL-GGIKFVLLRDRTGIVQLTLPKQKVPKETFEKVPKLTKESV 71 E G V + GWV RD GI FV + D + + L + E + LT + Sbjct: 17 EHIGRRVMINGWVRTRRDSKAGISFVEVNDGSCLKNLQVIVDHGRDRFQEILQSLTTGAS 76 Query: 72 IRVEGTVQANEKAPGGVEVIPQRIEVLSESDTHLPLDPTGKVDADLDTRLDARVLDLRRE 131 + + G V+ + VEV + I ++ D P K + + L R Sbjct: 77 VSITGVVRRSPAKGQPVEVEAESISIVGSCDP--ASYPLQKKRHSFEFLREIAHLRPRTN 134 Query: 132 EPQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV------YFERDA 185 A+ ++RN V+ A+ F +ERGF +HTP I S EG E+F V +F R Sbjct: 135 TIGAVMRVRNSVSYAVHRFFQERGFYYIHTPIITTSDCEGAGEVFRVTAQQDPEFFGRPT 194 Query: 186 YLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAISVDIEMSFIESEEDVMR 245 YL S QL ++ A +VY GP FRAE TRRHL+E ++ EM+F + E D + Sbjct: 195 YLTVSGQLQAEVY-ALALGKVYTFGPTFRAENSQTRRHLSEFWMIEPEMAFADLEND-LA 252 Query: 246 VLEELLAHVFRKVREECEKELE---------ALDRELPELETPFERITYEETLDLLSEHG 296 + ++ L HV V EC++EL+ L+R E PFE +TY E + LL + G Sbjct: 253 LAQDFLHHVVSSVMSECDEELQFFSKFFDEKLLERLQTVAERPFEVVTYTEAISLLKKSG 312 Query: 297 ----IEVEWGEDLPTEAERKLGE-IFEEPFFITEWPRETRPFYTMAKDDEVTTA-FDLMY 350 EWG DL E ER L E +F P + +PR+ +PFY DD T A D++ Sbjct: 313 ENFTYPAEWGCDLQAEHERYLTERVFNGPVAVIHFPRDIKPFYMKVNDDGRTVAAMDVLV 372 Query: 351 QGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAFKYGMPPHGGWGLGLERTLMT 409 G+ E+ G++RE+RY++L+ Q++ +G++PE + YL+ KYG PH G+GLGLER + Sbjct: 373 AGVGEIIGGSEREYRYELLLEQMKLKGMNPEAYEWYLDLRKYGSVPHAGFGLGLERLIQF 432 Query: 410 ITGAENIREVTLFPR 424 +TG NIRE FPR Sbjct: 433 LTGVPNIRETIPFPR 447 Lambda K H 0.318 0.138 0.397 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: 479 Number of extensions: 28 Number of successful extensions: 6 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: 431 Length of database: 454 Length adjustment: 32 Effective length of query: 399 Effective length of database: 422 Effective search space: 168378 Effective search space used: 168378 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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