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_057507926.1 ABB28_RS06830 asparagine--tRNA ligase
Query= curated2:Q8TXG4 (431 letters) >NCBI__GCF_001431535.1:WP_057507926.1 Length = 464 Score = 181 bits (460), Expect = 3e-50 Identities = 140/451 (31%), Positives = 209/451 (46%), Gaps = 50/451 (11%) Query: 15 DGEEVRLAGWVHEVRDLGGIKFVLLRDRTGIVQLTLPKQKVPKET---FEKVPKLTKESV 71 +G EV + GWV VR + F+ + D + P Q V E+ F+ V +LT Sbjct: 16 EGGEVTVRGWVRTVRGSANLAFINVTDGSCFA----PIQVVAAESLANFDAVKRLTSGCS 71 Query: 72 IRVEGTVQANEKAPGGVEVIPQRIEVLS--ESDTHLPLDPTGKVDADLDTRLDARVLDLR 129 + +GT+ ++ E+ +EV+ E P+ P L + L R Sbjct: 72 LIAKGTLVKSQGKGQSFEIQASDVEVVGWVEDPLTYPIQPKPMSPEFLR---EVAHLRPR 128 Query: 130 REEPQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV---------- 179 A+ +IRN ++ A+ F + GF + TP I S EG ++F V Sbjct: 129 TNLFGAVTRIRNCLSQAVHRFFHQNGFNWISTPIITTSDAEGAGQMFRVSTLDMVNLPRT 188 Query: 180 ----------YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAIS 229 +F ++ +L S QL + A +VY GP FRAE NT RHL E Sbjct: 189 ERGEVDFSRDFFGKETFLTVSGQLNVEAYCLA-LSKVYTFGPTFRAENSNTTRHLAEFWM 247 Query: 230 VDIEMSFIESEEDVMRVLEELLAHVFRKVREECEKELEALDRELPE---------LETPF 280 ++ E++F + ED R+ EE L ++FR V +E +L L + + + PF Sbjct: 248 IEPEIAFADLAEDA-RLAEEFLKYLFRAVLDERGDDLAFLAERVDKNAISKLENFINAPF 306 Query: 281 ERITYEETLDLLSEHG----IEVEWGEDLPTEAERKLGEI-FEEPFFITEWPRETRPFYT 335 E+I Y E + LL G VEWG DL TE ER L E P +T +P + FY Sbjct: 307 EQIDYTEAVKLLQNSGRKFDFPVEWGLDLQTEHERWLTEEHIGRPVVVTNYPEHIKAFYM 366 Query: 336 MAKDDEVTTA-FDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAFKYGM 393 DD T A D++ G+ E+ G+QRE R DVL ++ + GL E + Y + +YG Sbjct: 367 RLNDDGKTVAAMDVLAPGIGEIIGGSQREERLDVLDARMAQFGLDREHYGWYRDFRRYGS 426 Query: 394 PPHGGWGLGLERTLMTITGAENIREVTLFPR 424 PH G+GLG ER ++ + G NIR+ +PR Sbjct: 427 VPHAGFGLGFERLVVYVCGLSNIRDAIAYPR 457 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: 454 Number of extensions: 27 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: 464 Length adjustment: 33 Effective length of query: 398 Effective length of database: 431 Effective search space: 171538 Effective search space used: 171538 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