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_011320339.1 AVA_RS18405 asparagine--tRNA ligase
Query= curated2:Q8TXG4 (431 letters) >NCBI__GCF_000204075.1:WP_011320339.1 Length = 463 Score = 230 bits (587), Expect = 6e-65 Identities = 152/444 (34%), Positives = 226/444 (50%), Gaps = 40/444 (9%) Query: 17 EEVRLAGWVHEVRDLGGIKFVLLRDRTGIVQLTLPKQKVPKETFEKVPKLTKESVIRVEG 76 E + + GWV R+L G F+ + D + + L + + + V +L + + V G Sbjct: 17 ESLVVQGWVRTKRELKGFAFIEVNDGSSLGNLQVVINQDLPDYAVIVKQLNTGASVEVNG 76 Query: 77 TVQANEKAPGGVEVIPQRIEVLSESDTHLPLDPTGKVDADLDTRLDARVLDLRREEPQAI 136 + A++ +E+ + ++V E+D P K + L R A+ Sbjct: 77 VLVASQGKGQRIELKAEAVKVYGEADPETY--PLQKKRHSFEFLRTIGHLRSRTNSFGAV 134 Query: 137 FKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV----------------- 179 F++RN + AI +F +ERGF+ VHTP I AS EG ELF V Sbjct: 135 FRVRNACSAAIHQFFQERGFLWVHTPIITASDCEGAGELFSVTSLDLKQIPRTENQGIDY 194 Query: 180 ---YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAISVDIEMSF 236 +F + YL S QL ++ MA F VY GP FRAE NT RHL E V+ EM+F Sbjct: 195 SQDFFAKPTYLTVSGQLEAEV-MAMAFSNVYTFGPTFRAENSNTSRHLAEFWMVEPEMAF 253 Query: 237 IESEEDVMRVLEELLAHVFRKVREECEKELEALDRELPE---------LETPFERITYEE 287 + E D M + E L H+F V E+C +++E ++ + + FER+TY + Sbjct: 254 CDLEGD-MDLAEAFLKHIFNHVLEKCPEDMEFFNQRIDNTVLATAENIINNQFERLTYTD 312 Query: 288 TLDLLSEHGIEVE----WGEDLPTEAERKLGE-IFEEPFFITEWPRETRPFYTMAKDDEV 342 + LL + ++ E WG DL +E ER L E +F++P +T++P + + FY DDE Sbjct: 313 AIKLLEKADVKFEYPVSWGLDLQSEHERYLAEQLFKKPVIVTDYPAQIKAFYMRLSDDEK 372 Query: 343 TT-AFDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAFKYGMPPHGGWG 400 T A D++ + E+ G+QRE R DVL R+I QG+ PED YL+ +YG PH G+G Sbjct: 373 TVRAMDVLAPKIGEIIGGSQREERLDVLERRILAQGMQPEDLWWYLDLRRYGTVPHAGFG 432 Query: 401 LGLERTLMTITGAENIREVTLFPR 424 LG ER + ITG NIR+V FPR Sbjct: 433 LGFERLVQFITGMGNIRDVIPFPR 456 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: 456 Number of extensions: 28 Number of successful extensions: 7 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: 463 Length adjustment: 33 Effective length of query: 398 Effective length of database: 430 Effective search space: 171140 Effective search space used: 171140 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 09 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