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_013842764.1 DESRU_RS14175 asparagine--tRNA ligase
Query= curated2:A6USZ9 (438 letters) >NCBI__GCF_000215085.1:WP_013842764.1 Length = 430 Score = 254 bits (649), Expect = 4e-72 Identities = 145/422 (34%), Positives = 239/422 (56%), Gaps = 11/422 (2%) Query: 22 GQEIIIMGWNHSIRKLGKLVFIILRDREGTIQIVAPKQKVSEETFATAKSLGKEDVMAIK 81 G+E+ + GW ++ R GK+ F+ILRD G +Q V K + E F AK + +E + +K Sbjct: 15 GEEVTLQGWLYNKRSSGKIQFLILRDGTGLVQGVLAKNE-GPELFEKAKGITQESSLTVK 73 Query: 82 GKVVANEKAPAGFEVIPIEIKILNKADTPLPLDPSEKVSADIDTRLDKRFLDLRRPKIQS 141 G V ++ G+E+ ++I++ A+ P+ E +D +D+R L +R P+ + Sbjct: 74 GIVREEPRSVGGYELTITGLEIIHLAEE-YPITHKEH---GVDFLMDRRHLWMRTPRQTA 129 Query: 142 LFKLRSEVLKSIRNTFHDNGFIDVDTPKLVASATEGGTELFPISYFDKEAFLGQSPQLYK 201 + ++R+E+ ++ R+ FH++ F VD+P + +A EG T LF + Y ++A+L QS QLY Sbjct: 130 ILRIRAEIEQAARDFFHEHDFTLVDSPIITPAACEGTTTLFELDYHGEKAYLSQSGQLYN 189 Query: 202 QMMMAAGFDRVFEIGPIFRAEEHNTRRHLNEAISIDCEMSFADEKDAMEILEKVINNAFT 261 + A R++ GP FRAE+ TRRHL E I+ E +F D +D M++ E+++ Sbjct: 190 EAS-ALAVGRMYCFGPTFRAEKSKTRRHLMEFWMIEAEAAFFDHEDNMKLQEEMVYFIVR 248 Query: 262 DIYNNNQKELQTLGIDLKVQET---PFPRIEYTEAVDMVNAKGVEMEWGEDFSRPAEAAL 318 + +K+L+ LG D+ E PFPR+ YTEAV+++ KG E WG+DF P E + Sbjct: 249 RVLERRRKDLEFLGRDISKLEAVKLPFPRLSYTEAVELLKGKGEEFTWGDDFGAPHETII 308 Query: 319 GEMMDGFYFITDWPTEIRPFYTLPNEDNPKLCKAFDLMYKD--LEISSGAQRNHKYDLLV 376 E D FI +PTEI+ FY P+ ++P++ DL+ + E+ G QR LL Sbjct: 309 SESFDAPVFIHRFPTEIKAFYMKPDPEDPRVVLGADLIAPEGYGEMIGGGQRLDDLKLLE 368 Query: 377 EGIKRMGLNPEGFGTYLEAFKYGMPPHSGWGVGIERLMMIMACQQNIRECVLFPRDRQRL 436 + ++ L E F YL+ +YG PHSG+G+G+ER + + ++RE + +PR R+ Sbjct: 369 QRLEEHKLPKEAFEWYLDLRRYGSVPHSGFGLGLERTVAWICKLDHVRETIPYPRMLYRV 428 Query: 437 TP 438 P Sbjct: 429 YP 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: 471 Number of extensions: 21 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 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