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_092484312.1 BM299_RS11660 lysine--tRNA ligase
Query= curated2:C0R2C9 (586 letters) >NCBI__GCF_900115975.1:WP_092484312.1 Length = 503 Score = 120 bits (302), Expect = 1e-31 Identities = 85/285 (29%), Positives = 148/285 (51%), Gaps = 30/285 (10%) Query: 17 GKEVKLAGWVLRRRDHGGVIFVDLRDRTGFVQIV--FNPEISKEAHNDAQDLRSEYVISV 74 G++V LAG ++ +R HG F +L+D G +Q+ FN +I +EA++ L ++ V Sbjct: 64 GRQVTLAGRIMAKRGHGKASFANLQDSVGRIQLYARFN-DIGEEAYDLFTKLDIGDIVGV 122 Query: 75 EGKIRARSPEMINPKIPTGEIEVMVEKMELLNTSETPPFLLEDDIDTGEDIRLKYR--YL 132 GK+ K GE+ V + + LL+ S P L + D+ L+YR Y+ Sbjct: 123 TGKVF---------KTRMGEVTVAAQALRLLSKSLRP---LPEKWHGLRDVELRYRQRYV 170 Query: 133 DLR-RPTVFNNLYKRFQITNAFRKHLSDNGFIDVETPILNKSTPEG-ARDFLVPSRLNAG 190 DL P V KR +I +A R +L GF++VETP+++ AR F+ Sbjct: 171 DLIVNPGVKETFVKRSRIVHAIRNYLEQKGFLEVETPMMHPIAGGATARPFITHHNALDM 230 Query: 191 DFYALPQSPQIFKQILMIGGFDRYYQIAKCFRDEDLRADRQPEFTQVDIETSFLNTDEFL 250 D Y L +P+++ + L++GGFDR Y+I + FR+E + PEFT +++ ++ + ++ + Sbjct: 231 DLY-LRIAPELYLKRLLVGGFDRVYEINRNFRNEGISTKHNPEFTMLELYQAYADYNDMM 289 Query: 251 SIMENVTANIVKDVYG----------IDLPTPFPRLNYYDAMEMY 285 + E++ N+ K+V G I L P+ R+ +A++ Y Sbjct: 290 DLTEDLIYNVAKEVLGTSAVRYDDVEISLDKPWARVPMLEAVKKY 334 Score = 47.0 bits (110), Expect = 2e-09 Identities = 22/38 (57%), Positives = 28/38 (73%) Query: 519 LDALKYGAPPMCGMAYGIDRVVMLLQKQDSIREVIAFP 556 ++AL+YG PP G+ GIDR+VMLL SIR+VI FP Sbjct: 459 INALEYGMPPAGGLGIGIDRLVMLLTGSASIRDVILFP 496 Lambda K H 0.321 0.141 0.410 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: 697 Number of extensions: 41 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 586 Length of database: 503 Length adjustment: 35 Effective length of query: 551 Effective length of database: 468 Effective search space: 257868 Effective search space used: 257868 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: 52 (24.6 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