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_013450489.1 CALNI_RS01780 lysine--tRNA ligase
Query= curated2:Q980V3 (429 letters) >NCBI__GCF_000183405.1:WP_013450489.1 Length = 490 Score = 148 bits (374), Expect = 3e-40 Identities = 134/442 (30%), Positives = 225/442 (50%), Gaps = 47/442 (10%) Query: 18 EVKVAGWVHNVRNLGGKIFILLRDKSGIGQIVVEKGNNAYDKVINIGLESTIVVN--GVV 75 +V VAG + ++R+ G F ++D++G QI +++ + V I ++T V + G+ Sbjct: 51 KVTVAGRILSMRHFGKATFATIKDRTGSIQIYIKRDD--LTDVEKISFDNTDVGDFIGIS 108 Query: 76 KADARAPNG-VEVHAKDIEILSYARSPLPLDVTGKVKADIDTRLRERLLDLR-RLEMQAV 133 + G + ++A+ +IL+ A LP G DI+ R R+R +DL E++ V Sbjct: 109 GFLFKTKTGELTIYAETFKILTKALRDLPEKWHGL--KDIEIRQRQRYVDLIVNPEVKEV 166 Query: 134 LKIQSVAVKSFRETLYKHGFVEVFTPKIIASATEGGAQLFPVLY----FGKEAFLAQSPQ 189 K +S+ +K R+ Y F+EV TP + A GGA P + + +L +P+ Sbjct: 167 FKKRSLIIKHIRDFFYNKDFLEVETPMMHPIA--GGATAKPFITHHNTLDMKLYLRIAPE 224 Query: 190 LY-KELLAGAIERVFEIAPAWRAEESDTPYHLSEFISMDVEMAFADYNDIMALIEQIIYN 248 LY K L+ G ERVFEI +R E T H EF ++ A+ADY D+M + E++IY Sbjct: 225 LYLKRLVVGGFERVFEINRNFRNEGISTK-HNPEFTMIEWYQAYADYFDLMKMTEELIYE 283 Query: 249 M---INDVKRECENELKILNYTPP------------NVRIPIKKVSYSDAIELLKSKGVN 293 + IN + +I N TPP RIP ++S S L K+K +N Sbjct: 284 IALKINGTPIITFGDYEI-NLTPPWEKLTLEQAIEKYARIPEPELS-SYEFALNKAKELN 341 Query: 294 IKFGDDIGTPELRV-LYNELKEDLY----FVTDWPWLSRPFYTKQKKDNPQLSESFDLIF 348 IK D G ++ + ++ L ED F+ D+P P +K KKDNP+++E F+L Sbjct: 342 IKVEDGWGRGKIVLTIFETLVEDKLIQPTFIIDYPKEVSPL-SKSKKDNPEITERFELFI 400 Query: 349 RWLEIVSGSSRNHVK----EVLENSLKVRGLNPESFEF----FLKWFDYGMPPHAGFGMG 400 +E+ +G + + E E +K + E +++ +YG+PP AG G+G Sbjct: 401 AGMEVANGFNELNDPIDQYERFEKQVKAKEAGDEEAHMMDKDYIRALEYGLPPTAGEGLG 460 Query: 401 LARVMLMLTGLQSVKEVVPFPR 422 + R++++LT +S++EV+ FP+ Sbjct: 461 VDRLVMLLTDTKSIREVILFPQ 482 Lambda K H 0.320 0.138 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: 509 Number of extensions: 30 Number of successful extensions: 5 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: 429 Length of database: 490 Length adjustment: 33 Effective length of query: 396 Effective length of database: 457 Effective search space: 180972 Effective search space used: 180972 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