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_011462263.1 DHAF_RS24165 asparagine--tRNA ligase
Query= curated2:Q8TXG4 (431 letters) >NCBI__GCF_000021925.1:WP_011462263.1 Length = 463 Score = 207 bits (527), Expect = 5e-58 Identities = 143/453 (31%), Positives = 228/453 (50%), Gaps = 42/453 (9%) Query: 11 TPERDGEEVRLAGWVHEVRDLGGIKFVLLRDRTGIVQLTLPKQKVPKETFEKVPKLTKES 70 TP +E++++GWV +R F+ + D + + + ++ FE++ K+ S Sbjct: 13 TPAYLNQELQISGWVRTLRVSKSFGFIEINDGSFFKGIQVVFEE-DLNNFEEIAKVATGS 71 Query: 71 VIRVEGTVQANEKAPGGVEVIPQRIEVLSESDTHLPLDPTGKVDADLDTRLDARVLDLRR 130 + ++G + + A E+ Q I + PL L T R R Sbjct: 72 SLIIKGLLVESPGAKQPFELKAQSIMIEGACSGDYPLQKKRHSFEYLRTIAHLRP---RT 128 Query: 131 EEPQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV----------- 179 A+F++R++V AI +F +++GF+ +HTP I S EG E+F V Sbjct: 129 NTFAAVFRVRSLVAYAIHKFFQDKGFVYIHTPIITGSDAEGAGEMFRVTTLDLDALPRTE 188 Query: 180 ---------YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAISV 230 +F ++ L S QL + A F VY GP FRAE NT RH E + Sbjct: 189 EGRIDYAKDFFGKETNLTVSGQLNAETYCMA-FRNVYTFGPTFRAENSNTARHAAEFWMI 247 Query: 231 DIEMSFIESEEDVMRVLEELLAHVFRKVREECEKEL----EALDRELPE-----LETPFE 281 + E++F + ++D M + EE++ ++ V E +E+ E +D+ L + + + F Sbjct: 248 EPEIAFADLQDD-MELAEEMMKYLISYVLEHAPEEMAFFNEFVDKTLFDRLDNIVNSDFG 306 Query: 282 RITYEETLDLLSEHG----IEVEWGEDLPTEAERKLGE-IFEEPFFITEWPRETRPFYTM 336 R+TY E +++L + VEWG DL TE ER L E IF++P F+ ++P++ + FY Sbjct: 307 RLTYTEAIEILQKEKERFEFPVEWGADLQTEHERFLTEQIFKKPVFVVDYPKDIKAFYMR 366 Query: 337 AKDDEVTTA-FDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAFKYGMP 394 DD+ T A DL+ G+ E+ G+QRE R D L +++ E GL ED+ YL+ KYG Sbjct: 367 LNDDQKTVAAMDLLVPGVGEIIGGSQREERLDYLEKRMAELGLHKEDYSWYLDLRKYGGT 426 Query: 395 PHGGWGLGLERTLMTITGAENIREVTLFPRDRK 427 H G+GLG ER +M +TG NIR+V FPR K Sbjct: 427 RHAGYGLGFERVIMYLTGISNIRDVVAFPRTVK 459 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: 497 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: 431 Length of database: 463 Length adjustment: 33 Effective length of query: 398 Effective length of database: 430 Effective search space: 171140 Effective search space used: 171140 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