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 208934 DVU0007 asparaginyl-tRNA synthetase
Query= curated2:Q8TXG4 (431 letters) >MicrobesOnline__882:208934 Length = 461 Score = 196 bits (499), Expect = 1e-54 Identities = 143/443 (32%), Positives = 216/443 (48%), Gaps = 44/443 (9%) Query: 19 VRLAGWVHEVRDLGGIKFVLLRDRTGIVQL-TLPKQKVPKETFEKVPKLTKESVIRVEGT 77 +RL GWV RD G F+ + D + + + + + +P + + ++ + + + G Sbjct: 19 IRLCGWVRTRRDAKGFSFLEINDGSCLANIQAIVDEGIP--AYANIGAVSTGAAVDITGE 76 Query: 78 VQANEKAPGGVEVIPQRIEVLSESDTHL-PLDPTGKVDADLDTRLDARVLDLRREEPQAI 136 + + EV Q + +L +D PL D L + R R + A Sbjct: 77 LVESPGKGQKWEVRVQTLTLLGAADAETYPLQKKRHSDEFLRSIAHLRA---RTNKYGAA 133 Query: 137 FKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV----------------- 179 F+IR+ AI EF ERGF VHTP + S EG E+F V Sbjct: 134 FRIRSEAAFAIHEFYRERGFFYVHTPILTGSDCEGAGEMFRVTTLPVEGSATPASGNRYE 193 Query: 180 --YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAISVDIEMSFI 237 +F ++ L S QL + L A G +VY GP FRAE NT RH E ++ E++F Sbjct: 194 NDFFGKECNLTVSGQLEAETL-ALGLGKVYTFGPTFRAENSNTPRHAAEFWMIEPEVAFA 252 Query: 238 ESEEDVMRVLEELLAHVFRKVREECEKELEALDRELPEL---------ETPFERITYEET 288 + EED M + E++ V R++ + C +L+ +R + + PF R +Y E Sbjct: 253 DLEED-MNLAEDMTRTVVRRILDRCAADLDLFNRFVDTTLVERLRQIADEPFARCSYTEA 311 Query: 289 LDLLSEHGIEVEW----GEDLPTEAERKLGEI-FEEPFFITEWPRETRPFYTMAKDDEVT 343 ++LL + G + E+ G DL TE ER L E F +P + +P+E + FY DD T Sbjct: 312 IELLLKSGKKFEYPVSFGLDLQTEHERYLAEEHFGKPVIVYNYPKEIKAFYMRLNDDGRT 371 Query: 344 TA-FDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAFKYGMPPHGGWGL 401 A D++ + EL G+QRE R DVL +I E G + ED+ YL+ ++G PH G+G+ Sbjct: 372 VAAMDVLVPRIGELIGGSQREERLDVLEARINEMGQNLEDYWWYLDLRRFGSVPHAGFGM 431 Query: 402 GLERTLMTITGAENIREVTLFPR 424 G ER LM +TG NIR+V FPR Sbjct: 432 GFERLLMLLTGITNIRDVIPFPR 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: 460 Number of extensions: 32 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 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