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_010530794.1 ON01_RS09450 asparagine--tRNA ligase
Query= curated2:A6USZ9 (438 letters) >NCBI__GCF_000224785.1:WP_010530794.1 Length = 430 Score = 273 bits (698), Expect = 8e-78 Identities = 158/424 (37%), Positives = 245/424 (57%), Gaps = 11/424 (2%) Query: 21 DGQEIIIMGWNHSIRKLGKLVFIILRDREGTIQIVAPKQKVSEETFATAKSLGKEDVMAI 80 + Q++ I W + R GK+ F+ LRD G IQ V K V+EE F AK++ +E M I Sbjct: 12 EDQDVTIGVWLANKRSSGKIAFLQLRDGTGFIQGVVAKNDVTEEVFQLAKNMTQESSMYI 71 Query: 81 KGKVVANEKAPAGFEVIPIEIKILNKADTPLPLDPSEKVSADIDTRLDKRFLDLRRPKIQ 140 GK+V + ++P G+E+ +IK++ +A P+ P E + + +D R L LR + Sbjct: 72 SGKIVEDTRSPFGYEMQVKDIKLIQEA-VDYPITPKEHGTEFL---MDHRHLWLRSSRQH 127 Query: 141 SLFKLRSEVLKSIRNTFHDNGFIDVDTPKLVASATEGGTELFPISYFDKEAFLGQSPQLY 200 ++ K+R+E++++ F+D G++ VD P L S+ EG TELF YFD+EA+L QS QLY Sbjct: 128 AIMKVRNEIIRATYQFFNDQGYVKVDPPILTGSSAEGTTELFHTQYFDEEAYLSQSGQLY 187 Query: 201 KQMMMAAGFDRVFEIGPIFRAEEHNTRRHLNEAISIDCEMSFADEKDAMEILEKVINNAF 260 + A +VF GP FRAE+ TRRHL E I+ EM+F D ++++EI E+ ++ Sbjct: 188 ME-AAAMALGKVFSFGPTFRAEKSKTRRHLIEFWMIEPEMAFVDHEESLEIQEQYVSFVV 246 Query: 261 TDIYNNNQKELQTLGID---LKVQETPFPRIEYTEAVDMVNAKG-VEMEWGEDFSRPAEA 316 + N Q EL TLG D L+ + PFPRI Y A+ ++ KG ++EWGEDF P E Sbjct: 247 QSVLENCQLELNTLGRDTSKLEKIKAPFPRISYDGAIKLLKDKGFTDIEWGEDFGAPHET 306 Query: 317 ALGEMMDGFYFITDWPTEIRPFYTLPNEDNPKLCKAFDLMYKD--LEISSGAQRNHKYDL 374 A+ E + FIT++P +I+ FY P+ + ++ DL+ + E+ G+QR + L Sbjct: 307 AIAESFEKPVFITNYPADIKSFYMKPDPERSEVVLCADLIAPEGYGEVIGGSQRIDDFKL 366 Query: 375 LVEGIKRMGLNPEGFGTYLEAFKYGMPPHSGWGVGIERLMMIMACQQNIRECVLFPRDRQ 434 + + + L + YLE +YG PHSG+G+G+ER + +A ++RE + FPR Sbjct: 367 MEQRYEEHNLTGPAYKWYLELRQYGSVPHSGFGLGLERTVAWIAGVDHVRETIPFPRLLN 426 Query: 435 RLTP 438 RL P Sbjct: 427 RLYP 430 Lambda K H 0.320 0.137 0.405 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: 455 Number of extensions: 27 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: 438 Length of database: 430 Length adjustment: 32 Effective length of query: 406 Effective length of database: 398 Effective search space: 161588 Effective search space used: 161588 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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