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_011988714.1 CKL_RS00580 asparagine--tRNA ligase
Query= curated2:Q8TXG4 (431 letters) >NCBI__GCF_000016505.1:WP_011988714.1 Length = 463 Score = 225 bits (573), Expect = 3e-63 Identities = 154/446 (34%), Positives = 226/446 (50%), Gaps = 46/446 (10%) Query: 17 EEVRLAGWVHEVRDLGGIKFVLLRDRTGI--VQLTLPKQKVPKETFEKVPKLTKESVIRV 74 +++ ++GW+ +RD F+ L D + VQ+ L + E F+++ KL S + V Sbjct: 19 KDIEISGWIRTIRDSKSFAFIELNDGSFFKNVQVVLDDKI---ENFKEIIKLPISSSLSV 75 Query: 75 EGTVQANEKAPGGVEVIPQRIEVLSESDTHLPLDPTGKVDADLDTRLDARVLDLRREEPQ 134 EGT+ A E+ ++I + S + PL L T R R Sbjct: 76 EGTLILTPNAKQSFEIKAKKISLEGNSSSEYPLQKKRHTLEYLRTIAHLRP---RSNTFS 132 Query: 135 AIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV--------------- 179 A+F++R++ A+ +F +E+ F+ V+TP I S EG E+F + Sbjct: 133 AVFRVRSIAAYAVHKFFQEKDFVYVNTPIITGSDCEGAGEMFRITTMDLNNVPKEEDNSV 192 Query: 180 -----YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAISVDIEM 234 +F ++ L S QL + MA F VY GP FRAE+ NT RH E ++ EM Sbjct: 193 DFSKDFFGKETNLTVSGQLSAET-MALAFRNVYTFGPTFRAEDSNTSRHAAEFWMIEPEM 251 Query: 235 SFIESEEDVMRVLEELLAHVFRKVREECEKEL---------EALDRELPELETPFERITY 285 +F E + D M EEL+ ++ V E+ +E+ DR + + F RITY Sbjct: 252 AFAELK-DYMDTAEELVKYIINYVLEKAPEEMAFFNSFIDKSLFDRLNNVVNSEFGRITY 310 Query: 286 EETLDLLSEHGIE----VEWGEDLPTEAERKLGE-IFEEPFFITEWPRETRPFYTMAKDD 340 E +D+L + G VEWG DL TE ER L E +FE+P F+T++P+ + FY +D Sbjct: 311 TEAVDILQKSGASFQYPVEWGIDLQTEHERYLTEKVFEKPIFVTDYPKAIKAFYMRENED 370 Query: 341 EVTTAF-DLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAFKYGMPPHGG 398 T A DL+ G+ E+ G+QRE R VL ++I E GL+ ED+ YLE KYG H G Sbjct: 371 GKTVAAADLLVPGVGEIVGGSQREERLSVLEKRISEFGLNKEDYWWYLELRKYGETKHSG 430 Query: 399 WGLGLERTLMTITGAENIREVTLFPR 424 +GLG ER LM ITG NIR+V FPR Sbjct: 431 FGLGFERILMYITGMSNIRDVIPFPR 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: 463 Number of extensions: 26 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 09 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