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_041230115.1 DACET_RS03775 asparagine--tRNA ligase
Query= curated2:Q8TXG4 (431 letters) >NCBI__GCF_000025725.1:WP_041230115.1 Length = 454 Score = 198 bits (504), Expect = 2e-55 Identities = 154/460 (33%), Positives = 225/460 (48%), Gaps = 45/460 (9%) Query: 2 LKDAYTADVTPERDGEEVRLAGWVHEVRDLGGIKFVLLRDRTGIVQLTLPKQKVPKE--- 58 +KD A+ PE D + + GWV RD F+ L D + + L Q + E Sbjct: 6 IKDLLNAE-HPESD---ITVHGWVRSKRDSKNFTFLELNDGSCLKNL----QAIADEDIG 57 Query: 59 TFEKVPKLTKESVIRVEGTVQANEKAPGGVEVIPQRIEVLSESDTHL-PLDPTGKVDADL 117 T++ + + + + ++G + + E+ + + ++ +D PL D L Sbjct: 58 TYDVLKDINTGASVEIKGDLIESPGKGQKWELKAKAVALVGGADQETYPLQKKRHSDEFL 117 Query: 118 DTRLDARVLDLRREEPQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFP 177 R R + AIF+IR+ + A+ +F ERGF VHTP I S EG ++F Sbjct: 118 RQIAHLRP---RTNKYGAIFRIRSEASFAVHQFFRERGFHYVHTPIITGSDCEGAGQMFR 174 Query: 178 VV------------YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLN 225 V +F + AYL S QL + A VY GP FRAE NT RH Sbjct: 175 VTTLEDTKKPVAEDFFGKAAYLTVSGQLDAESY-ACALGSVYTFGPTFRAENSNTPRHAA 233 Query: 226 EAISVDIEMSFIESEEDVMRVLEELLAHVFRKVREECEKELEA----LDRELPE-----L 276 E ++ EM+F + ++ M + EE + ++ + E C+++LE +D+EL L Sbjct: 234 EFWMIEPEMAFADIHDN-MTLAEEFVKYLIWFLMENCKEDLELFFNFVDKELEAKLTNML 292 Query: 277 ETPFERITYEETLDLLSEHGIEVEW----GEDLPTEAERKLGEI-FEEPFFITEWPRETR 331 FER+ Y E + +L G + E+ G DL TE ER L E F++P F+ +P+ + Sbjct: 293 TNDFERVEYREAVKILENSGEKFEYPVGFGVDLQTEHERYLTEKHFKKPVFVYNYPKSIK 352 Query: 332 PFYTMAKDD-EVTTAFDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAF 389 PFY DD E A DL+ + EL G+QRE R DVL IE+ GLS E++ Y E Sbjct: 353 PFYMRQNDDGETVAAMDLLVPSVGELIGGSQREERLDVLDSAIEKMGLSMEEYGWYAELR 412 Query: 390 KYGMPPHGGWGLGLERTLMTITGAENIREVTLFPRDRKRL 429 KYG PH G+GLG ER LM +TG NIR+V F R K L Sbjct: 413 KYGTVPHAGFGLGFERLLMFVTGVTNIRDVIPFARTPKNL 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: 478 Number of extensions: 24 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: 454 Length adjustment: 32 Effective length of query: 399 Effective length of database: 422 Effective search space: 168378 Effective search space used: 168378 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