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 8501354 DvMF_2087 asparaginyl-tRNA synthetase (RefSeq)
Query= curated2:Q8TXG4 (431 letters) >FitnessBrowser__Miya:8501354 Length = 471 Score = 194 bits (493), Expect = 5e-54 Identities = 147/455 (32%), Positives = 213/455 (46%), Gaps = 47/455 (10%) Query: 10 VTPERDGEEVRLAGWVHEVRDLGGIKFVLLRDRTGIVQLT-LPKQKVPKETFEKVPKLTK 68 +T + +R+ GWV RD G F+ + D + + + + + +P F + + Sbjct: 17 LTAQAPVAHIRICGWVRTRRDAKGFSFLEINDGSCLANIQCIVDEALPD--FAVIKDVNT 74 Query: 69 ESVIRVEGTVQANEKAPGGVEVIPQRIEVLSESDTHL-PLDPTGKVDADLDTRLDARVLD 127 + + V G + + EV + +L +D PL D L T R Sbjct: 75 GAAVDVRGELVESPGKGQKWEVRAAALTLLGGADAEAYPLQKKRHSDEFLRTIAHLRA-- 132 Query: 128 LRREEPQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV-------- 179 R + A F+IR+ AI EF ERGF VHTP + S EG E+F V Sbjct: 133 -RTNKFGAAFRIRSEAAYAIHEFFRERGFFHVHTPILTGSDCEGAGEMFRVTTLPVSGAS 191 Query: 180 --------------YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLN 225 +F ++ L S QL + L A G +VY GP FRAE NT RH Sbjct: 192 GTPVPPSGNHFEADFFGKECNLTVSGQLEAEAL-AMGLGKVYTFGPTFRAENSNTARHAA 250 Query: 226 EAISVDIEMSFIESEEDVMRVLEELLAHVFRKVREECEKELEALDRE-----LPELET-- 278 E ++ E +F + +D M + E + V +V E C ++E DR + L T Sbjct: 251 EFWMIEPEFAFADLNDD-MELAEAMTRTVVTRVLERCAADIELFDRFVDNGLIERLRTIA 309 Query: 279 --PFERITYEETLDLLSEHGIE----VEWGEDLPTEAERKLGEI-FEEPFFITEWPRETR 331 PF R++Y E ++LL G + V +G DL TE ER L E F +P + +P+ + Sbjct: 310 GQPFARVSYREAIELLKACGKKFDYPVSFGLDLQTEHERYLAEEHFGKPVIVYNYPKSIK 369 Query: 332 PFYTMAKDD-EVTTAFDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAF 389 FY DD E A D++ + EL G+QRE R DVL +I E G +P D+ YL+ Sbjct: 370 AFYMRLNDDNETVAAMDVLVPRIGELIGGSQREERLDVLEARIREIGQNPGDYWWYLDLR 429 Query: 390 KYGMPPHGGWGLGLERTLMTITGAENIREVTLFPR 424 ++G PH G+GLG ER LM +TG NIR+V FPR Sbjct: 430 RFGSVPHAGFGLGFERLLMLLTGIANIRDVVPFPR 464 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: 458 Number of extensions: 29 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: 471 Length adjustment: 33 Effective length of query: 398 Effective length of database: 438 Effective search space: 174324 Effective search space used: 174324 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