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_011426870.1 RHE_RS18700 lysine--tRNA ligase
Query= curated2:B1GZY6 (584 letters) >NCBI__GCF_000092045.1:WP_011426870.1 Length = 498 Score = 94.7 bits (234), Expect = 8e-24 Identities = 88/279 (31%), Positives = 133/279 (47%), Gaps = 32/279 (11%) Query: 19 IAVCGWVHSRRDHGGVIFIDLRDREGILQIVFQPE--NKEIFEAAEKLRSEYVIAVKGWV 76 + V G V+S R+ G +F+D+ D G +QI + +E + +I V G V Sbjct: 63 VTVAGRVYSSRNSG--MFMDIHDASGKIQIFSHKDVTGEEARALLPMIDIGDIIGVTGIV 120 Query: 77 RNRPFGTLNTNMSTGNVELVAVELKILNTSPGLPFEISDYIDTSEELRLKYRYLD-LRRP 135 R G L T N + + + K L P +SD ELR + R+LD L Sbjct: 121 RRTKRGEL-----TINAQKIEMLTKSLLPMPEKWHGLSDI-----ELRYRKRHLDILTNE 170 Query: 136 NLQKNFVMRHKISKEIRNFLNEEGFLEIETPFLTKSTPEGARDFLVPSRLHHGNF---FA 192 + + F R KI IR F+ +GF+E+ETP L +S GA P + HH Sbjct: 171 DSKLRFQQRSKIVSGIRRFMENDGFMEVETPML-QSIYGGAT--AEPFKTHHNTLKLDMY 227 Query: 193 LPQSPQLF-KQILMSAGFDKYYQIVRCFRDEDLRADRQPEFTQVDVEMSFVDEEDVMVVI 251 L +P+LF K+ L+S DK ++I R FR+E + PEFT ++ ++ D ED+M ++ Sbjct: 228 LRIAPELFLKRTLVSGLTDKVFEINRNFRNEGVSTRHNPEFTMMECYWAYADYEDMMDLV 287 Query: 252 ERM---LARVFKMTLNLD-------IKMPFERMPYSEAM 280 ER+ LA T D K PF+R+P +A+ Sbjct: 288 ERLFETLALSIHGTTEFDFGDKRLSFKGPFKRVPMPDAV 326 Score = 50.1 bits (118), Expect = 2e-10 Identities = 35/118 (29%), Positives = 53/118 (44%), Gaps = 5/118 (4%) Query: 448 HPFTLPKDADSLTKENAGRAK-AKAYDVVLNGIELGGGSIRIHKSGIQKK-IFNILDISD 505 H PKD KE G + + ++ N ELG ++ Q++ + L+ + Sbjct: 381 HVTHFPKDISPFAKEVPGEPRLVERFETYCNAWELGNAFSELNDPEEQRRRMVEQLEQAH 440 Query: 506 ESAEKKFGF---LLKALTYGAPPHGGAALGFDRLCALISGEDSIREVIAFPKTQKAVD 560 EK+ L A+ G PP GG +G DRL L++ SIR+VI FP + D Sbjct: 441 ARGEKEKQLDEEFLDAIDQGMPPAGGLGIGVDRLIMLLTNAPSIRDVILFPARRSKAD 498 Lambda K H 0.320 0.139 0.404 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: 609 Number of extensions: 25 Number of successful extensions: 3 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: 584 Length of database: 498 Length adjustment: 35 Effective length of query: 549 Effective length of database: 463 Effective search space: 254187 Effective search space used: 254187 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