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 CA265_RS05115 CA265_RS05115 asparagine--tRNA ligase
Query= curated2:Q8TXG4 (431 letters) >FitnessBrowser__Pedo557:CA265_RS05115 Length = 482 Score = 197 bits (501), Expect = 6e-55 Identities = 141/468 (30%), Positives = 227/468 (48%), Gaps = 72/468 (15%) Query: 18 EVRLAGWVHEVRDLGGIKFVLLRDRTGI--VQLTLPKQKVPKETFEKVPKLTKESVIRVE 75 EV + GWV R+ +F+ L D + + +Q+ + +P E +++ T + I Sbjct: 19 EVTVMGWVRTFRNN---QFIALNDGSCMSNIQVVIDFNNLPDELLKRI---TTGAAISAT 72 Query: 76 GTVQANEKAPGGVEVIPQRIEVLSESDTH-LPLDPTGKVDADLDTRLDARVLDLRREEPQ 134 G + + VE+ +E+L +SD PL P L+ + L R Sbjct: 73 GKLIESLGKGQSVEIKATSVEILGDSDPEKFPLQPKKH---SLEFLREIAHLRFRTNTFN 129 Query: 135 AIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV--------------- 179 A+FK+R+ + AI +F ERGF+ +HTP I AS EG E+F V Sbjct: 130 AVFKVRHALAFAIHQFYNERGFVYMHTPVITASDAEGAGEMFKVTTLDFDNTPRSEDGKV 189 Query: 180 -----YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAISVDIEM 234 +F R L S QL + L A F ++Y GP FRAE NT RHL E ++ E+ Sbjct: 190 DFSQDFFARATNLTVSGQLEGE-LAAMAFGQIYTFGPTFRAENSNTTRHLAEFWMIEPEV 248 Query: 235 SFIESEEDVMRVLEELLAHVFRKVREECEKELEALDRELPE------------------- 275 +F + E++ M++ E+++ +V + + C+ ELE L+ L E Sbjct: 249 AFADLEDN-MQLAEDMMKYVIKYALDHCKDELEFLNTRLAEEDKQKPQNERSEFSLLEKL 307 Query: 276 ---LETPFERITYEETLDLLSEHG---------IEVEWGEDLPTEAERKLGEI-FEEPFF 322 L FER+TY E + +L + EWG DL +E ER L E F++P Sbjct: 308 DFCLANEFERLTYTEAIRILKSSKPNQKKQFKYLIDEWGADLQSEHERYLVEKHFKKPVI 367 Query: 323 ITEWPRETRPFYTM-----AKDDEVTTAFDLMYQGL-ELASGAQREHRYDVLVRQIEEQG 376 +T++P + + FY A+ + A D+++ G+ E+ G+QRE R D L +++E+ Sbjct: 368 LTDYPADIKSFYMRQNEPDAEGRQTVAAMDILFPGIGEMIGGSQREERLDRLTKRMEDLN 427 Query: 377 LSPEDFRHYLEAFKYGMPPHGGWGLGLERTLMTITGAENIREVTLFPR 424 + ++ YL+ ++G PH G+GLG ER ++ +TG NIR+V FPR Sbjct: 428 IPQDELWWYLDTRRFGSAPHSGFGLGFERLVLFVTGMTNIRDVIAFPR 475 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: 477 Number of extensions: 29 Number of successful extensions: 7 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: 482 Length adjustment: 33 Effective length of query: 398 Effective length of database: 449 Effective search space: 178702 Effective search space used: 178702 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