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_035235489.1 Q366_RS00900 asparagine--tRNA ligase
Query= curated2:Q8TXG4 (431 letters) >NCBI__GCF_000745975.1:WP_035235489.1 Length = 459 Score = 196 bits (497), Expect = 2e-54 Identities = 144/440 (32%), Positives = 218/440 (49%), Gaps = 38/440 (8%) Query: 18 EVRLAGWVHEVRDLGGIKFVLLRDRTGIVQLTLPKQKVPKETFEKVPKLTKESVIRVEGT 77 EV + GWV RD F+ L D + + + + E + +V KLT S V G Sbjct: 18 EVFVQGWVRTKRDAKDFSFIELNDGSCLANIQVIAGNDLSE-YNQVEKLTTGSAAGVTGQ 76 Query: 78 VQANEKAPGGVEVIPQRIEVLSESDTHLPLDPTGKVDADLDTRLDARVLDLRREEPQAIF 137 + + E+ ++V+S + + PL D L + R R + A F Sbjct: 77 LVESPGKGQKWEIRATAVDVISIAPENYPLQKKRHTDEFLRSIAHLRP---RTNKYGAAF 133 Query: 138 KIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV------------------ 179 +IR+ + AI F ++GF +H+P I S EG E+F V Sbjct: 134 RIRSRMAQAIHTFYLDKGFYYLHSPLITGSDCEGAGEMFRVTGLDPADVQKQGKMDFSRD 193 Query: 180 YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAISVDIEMSFIES 239 +F R+A L S QL +M A VY P FRAE NTRRH E ++ EM+F + Sbjct: 194 FFGREANLTVSGQLSAEMF-ALSLGDVYTFSPAFRAENSNTRRHAAEFWMLEPEMAFCDL 252 Query: 240 EEDV---MRVLEELLAHVFRKVREECEKELEALDREL-PELET----PFERITYEETLDL 291 + D+ +++ L+ H RE+ + + +D+ L P+LET PF R+ Y + + + Sbjct: 253 DGDMDHAEELVKYLVGHAMDHCREDLDLFMHFVDKTLGPQLETLVSKPFARLPYTQAVKI 312 Query: 292 LSEHG----IEVEWGEDLPTEAERKLGEI-FEEPFFITEWPRETRPFYTMAKDDEVTTA- 345 L + G V +G DL +E ER L E F+ P F+T++P++ +PFY DD T A Sbjct: 313 LKKCGKTFEYPVAYGIDLQSEHERFLAEEHFKTPVFLTDYPKQIKPFYMRMNDDGTTVAA 372 Query: 346 FDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAFKYGMPPHGGWGLGLE 404 DL+ G+ EL G+QRE R L +++E GL + + YL++ ++G PH G+G+G E Sbjct: 373 MDLLVPGIGELIGGSQREERLGPLEARMDEMGLDKDAYWWYLDSRRFGTVPHAGFGMGFE 432 Query: 405 RTLMTITGAENIREVTLFPR 424 R LM ITG NIR+V FPR Sbjct: 433 RFLMMITGISNIRDVIAFPR 452 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: 471 Number of extensions: 22 Number of successful extensions: 4 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: 459 Length adjustment: 32 Effective length of query: 399 Effective length of database: 427 Effective search space: 170373 Effective search space used: 170373 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