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 NP_349854.1 CA_C3260 asparaginyl-tRNA synthetase
Query= curated2:Q8TXG4 (431 letters) >NCBI__GCF_000008765.1:NP_349854.1 Length = 463 Score = 220 bits (561), Expect = 6e-62 Identities = 150/451 (33%), Positives = 226/451 (50%), Gaps = 42/451 (9%) Query: 10 VTPERDGEEVRLAGWVHEVRDLGGIKFVLLRDRTGIVQLTLPKQKVPKETFEKVPKLTKE 69 ++ E G++VRL+GWV +R F+ + D + + + + F+++ K Sbjct: 12 LSSEFGGKKVRLSGWVRTIRASKSFGFIEINDGSFFKNIQVVFDD-KLDNFKEISKFIIS 70 Query: 70 SVIRVEGTVQANEKAPGGVEVIPQRIEVLSESDTHLPLDPTGKVDADLDTRLDARVLDLR 129 S I VEG A E+ + I + SD PL K L+ L R Sbjct: 71 STITVEGEFVLTPNAKQPFEIHAENITLEGNSDNDYPLQ---KKRHTLEYLRSIAHLRPR 127 Query: 130 REEPQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV---------- 179 A+F++R++ A+ +F +ER F+ V+TP I AS EG E+F V Sbjct: 128 SNTFSAVFRVRSLAAYAVHKFFQERDFVYVNTPLITASDAEGAGEMFQVTTLDLKNPPKN 187 Query: 180 ----------YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAIS 229 +F + A L S QL + A F VY GP FRAEE NT RH E Sbjct: 188 EEGNIDFSKDFFGKKANLTVSGQLSAETF-ALAFRNVYTFGPTFRAEESNTTRHAAEFWM 246 Query: 230 VDIEMSFIESEEDVMRVLEELLAHVFRKVREECEKELEALDRELPE---------LETPF 280 ++ EM+F E D + EE++ ++ V E +E+E + + + + + F Sbjct: 247 IEPEMAFAELS-DYLDTAEEMVKYIINFVMENAPEEMEFFNTRIDKGLFDRLHNVVNSEF 305 Query: 281 ERITYEETLDLLSEHGIE----VEWGEDLPTEAERKLGE-IFEEPFFITEWPRETRPFYT 335 RITY E +D+L + G + V+WG DL TE ER L + +F++P F+T++P++ + FY Sbjct: 306 GRITYTEAVDILEKSGEKFEYPVKWGIDLQTEHERYLTDKVFKKPLFVTDYPKDIKAFYM 365 Query: 336 MAKDDEVTTAF-DLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAFKYGM 393 DD T A DL+ G+ E+ G+QRE R VL +++EE L+ ED+ YLE KYG Sbjct: 366 RINDDNKTVAAADLLVPGVGEIIGGSQREERLAVLEKRMEELNLNKEDYWWYLELRKYGE 425 Query: 394 PPHGGWGLGLERTLMTITGAENIREVTLFPR 424 H G+GLG ER +M +TG NIR+V FPR Sbjct: 426 TKHSGYGLGFERMIMYLTGISNIRDVIPFPR 456 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: 451 Number of extensions: 21 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: 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