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 5209429 Shew_1900 asparaginyl-tRNA synthetase (RefSeq)
Query= curated2:Q8TXG4 (431 letters) >FitnessBrowser__PV4:5209429 Length = 466 Score = 183 bits (465), Expect = 8e-51 Identities = 141/458 (30%), Positives = 220/458 (48%), Gaps = 58/458 (12%) Query: 16 GEEVRLAGWVHEVRDL-GGIKFVLLRDRT------GIVQLTLPKQKVPKETFEKVPKLTK 68 G +V + GWV RD GI F+ + D + G+V +L +++ +LT Sbjct: 17 GSQVTVRGWVRTRRDSKAGISFLAVYDGSCFDPIQGVVPNSLDNYN------DEILRLTA 70 Query: 69 ESVIRVEGTVQANEKAPGGVEVIPQRIEV---LSESDTHLPLDPTGKVDADLDTRLDARV 125 + + G + + E+ ++EV + + DT+ P ++ + Sbjct: 71 GCSVVMTGELVESPGKGQAFEMQVTKVEVTGWVEDPDTY----PMAAKRHSIEHLRELAH 126 Query: 126 LDLRREEPQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV------ 179 L R A+ ++RN ++ AI F E GFI V TP I AS EG E+F V Sbjct: 127 LRPRTNIIGAVARVRNCLSHAIHNFYNEEGFIWVSTPLITASDCEGAGEMFRVSTLDLEN 186 Query: 180 --------------YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLN 225 +F ++++L S QL + A ++Y GP FRAE NT RHL Sbjct: 187 LPRTDDGKVDFSEDFFGKESFLTVSGQLNGETY-ACALSKIYTFGPTFRAENSNTSRHLA 245 Query: 226 EAISVDIEMSFIESEEDVMRVLEELLAHVFRKVREECEKELE---------ALDRELPEL 276 E V+ E++F + DV + E +L + FR V E +LE ++R + Sbjct: 246 EFWMVEPEVAFADLN-DVAGLAERMLKYCFRAVLNERRDDLEFFAQRVDKTVIERLESFV 304 Query: 277 ETPFERITYEETLDLLSEHG----IEVEWGEDLPTEAERKLGEI-FEEPFFITEWPRETR 331 + F ++ Y + +++L G +VEWG DL +E ER L E F+ P + +P++ + Sbjct: 305 NSDFAQVDYTDAIEILKSCGKKFEFDVEWGIDLQSEHERYLAEEHFKAPVVVKNYPKDIK 364 Query: 332 PFYTMAKDDEVTTA-FDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAF 389 FY +D T A D++ G+ E+ GAQRE R DVL +++E GLS ED+ Y + Sbjct: 365 AFYMRLNEDGKTVAAMDVLAPGIGEIIGGAQREERLDVLDTRLDEMGLSKEDYWWYRDLR 424 Query: 390 KYGMPPHGGWGLGLERTLMTITGAENIREVTLFPRDRK 427 +YG PH G+GLG ER + +TG NIR+V FPR K Sbjct: 425 RYGTVPHSGFGLGFERLVSYVTGVSNIRDVIPFPRAPK 462 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: 491 Number of extensions: 36 Number of successful extensions: 5 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: 466 Length adjustment: 33 Effective length of query: 398 Effective length of database: 433 Effective search space: 172334 Effective search space used: 172334 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