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_011939799.1 GURA_RS15055 asparagine--tRNA ligase
Query= curated2:Q8TXG4 (431 letters) >NCBI__GCF_000016745.1:WP_011939799.1 Length = 461 Score = 190 bits (482), Expect = 9e-53 Identities = 138/453 (30%), Positives = 221/453 (48%), Gaps = 41/453 (9%) Query: 7 TADVTPERDGEEVRLAGWVHEVRDLGGIKFVLLRDRTGIVQLTLPKQKVPKETFEKVPKL 66 +A + R GEE+ L GWV VR + F+ + D + + L + + ++ V ++ Sbjct: 8 SAALAASRPGEELVLKGWVRTVRVGKDVTFLAINDGSCMTSLQVVVEPA-LPNYQDVCRI 66 Query: 67 TKESVIRVEGTVQANEKAPGGVEVIPQRIEVLSESDTHLPLDPTGKVDADLDTRLDARVL 126 S + V G ++ + A E+ + +E++ +D PL L T R Sbjct: 67 GTGSAVAVRGILRESPAAGQKYELAAEELEIIGPADDSYPLQKKRHSFEYLRTIAHLRP- 125 Query: 127 DLRREEPQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV------- 179 R A+F++R+ + A+ F ERGF+ VHTP I A+ EG ELF V Sbjct: 126 --RTNTFGAVFRVRSSLAQAVHRFFAERGFLYVHTPIITANDCEGAGELFRVTTLDMARP 183 Query: 180 ------------YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEA 227 +F + L S QL + L A F +Y GP FRAE NT RH E Sbjct: 184 PLAAGEVDYSGDFFAQATGLTVSGQLEGE-LFAQAFSDIYTFGPTFRAENSNTARHAAEF 242 Query: 228 ISVDIEMSFIESEEDVMRVLEELLAHVFRKVREECEKEL----EALDRELPE-----LET 278 ++ E++F + D + E+ L + R V + C +++ E +D+ L E ++ Sbjct: 243 WMIEPELAFADLMADAA-LAEDFLKFLCRHVLDNCGEDMAFFNEQIDKGLLERVRAVADS 301 Query: 279 PFERITYEETLDLLSEHGIE----VEWGEDLPTEAERKLGE-IFEEPFFITEWPRETRPF 333 F + Y E + L + + VEWG DL +E ER + E + P F+ +P++ + F Sbjct: 302 SFAVMEYTEAITHLKKAKVPFAFPVEWGLDLQSEHERYITEKVVGGPVFLVNYPKDIKAF 361 Query: 334 YTMAKDDEVTTA-FDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAFKY 391 Y DD T A DL+ + E+ G+QRE R D+L+ ++ + G++ + YL++ ++ Sbjct: 362 YMRQNDDGKTVAAMDLLVPKVGEIIGGSQREERLDLLLERMAQMGINEDGLWWYLDSRRW 421 Query: 392 GMPPHGGWGLGLERTLMTITGAENIREVTLFPR 424 G PH G+GLG ER LM +TG ENIR+V FPR Sbjct: 422 GSCPHAGFGLGFERLLMYLTGMENIRDVIPFPR 454 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: 455 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: 461 Length adjustment: 32 Effective length of query: 399 Effective length of database: 429 Effective search space: 171171 Effective search space used: 171171 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 12 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