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 Echvi_0072 Echvi_0072 asparaginyl-tRNA synthetase
Query= curated2:Q8TXG4 (431 letters) >FitnessBrowser__Cola:Echvi_0072 Length = 483 Score = 209 bits (531), Expect = 2e-58 Identities = 142/466 (30%), Positives = 228/466 (48%), Gaps = 65/466 (13%) Query: 16 GEEVRLAGWVHEVRDLGGIKFVLLRDRTGI--VQLTLPKQKVPKETFEKVPKLTKESVIR 73 G+ + GWV R + F+ + D + I Q+ + +E +++ T + I+ Sbjct: 19 GKNTTIMGWVRTKRGNKNVSFIAVNDGSTIQNYQVVADPNVISEEVLKRI---TTGACIK 75 Query: 74 VEGTVQANEKAPGGVEVIPQRIEVLSESDTH-LPLDPTGKVDADLDTRLDARVLDLRREE 132 G V A++ A E+I Q+IEVL E+D PL P ++ + L +R Sbjct: 76 ATGEVVASQGAGQDSELIAQKIEVLGEADADKYPLQPKKH---SMEFLRENAHLRMRTNT 132 Query: 133 PQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV------------- 179 A+F++R+ + A+ ++ ++GF +HTP I AS EG E F V Sbjct: 133 FGAVFRVRHALAFAVHQYFNDKGFFYIHTPIITASDAEGAGETFRVSTLDMKNPPLTEDG 192 Query: 180 -------YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAISVDI 232 +FER+ L S QL + L A +Y GP FRAE NT RHL E ++ Sbjct: 193 AVDYTKDFFERETNLTVSGQLEGE-LAAMALAEIYTFGPTFRAENSNTTRHLAEFWMIEP 251 Query: 233 EMSFIESEEDVMRVLEELLAHVFRKVREECEKELEALDRELPE----------------- 275 EM+F ++E++ + E+ L ++ E C+ +LE LD+ E Sbjct: 252 EMAFYDAEDN-QDLAEDFLKYIISYAMEHCKADLEFLDKRAAEENAKKPTNERTELGLLD 310 Query: 276 -----LETPFERITYEETLDLLSEHG---------IEVEWGEDLPTEAERKLGEI-FEEP 320 ++ FERI+Y E +++L I EWG DL +E ER L E F++P Sbjct: 311 RLRFVVDHDFERISYTEAIEILKNSKPNKKKKFSYIIDEWGADLQSEHERFLVEKHFKKP 370 Query: 321 FFITEWPRETRPFYTMAKDDEVTTA-FDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLS 378 +T++P++ + FY DD T A D+++ G+ E+ G+QRE + L +++E G+S Sbjct: 371 VILTDYPKDIKAFYMKQNDDGKTVAAMDILFPGIGEIVGGSQREENMEKLTTRMDEMGIS 430 Query: 379 PEDFRHYLEAFKYGMPPHGGWGLGLERTLMTITGAENIREVTLFPR 424 E+ YL+ ++G PH G+GLG ER + +TG NIR+V FPR Sbjct: 431 QEELYWYLDTRRFGATPHSGFGLGFERMVQFVTGMGNIRDVIAFPR 476 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: 476 Number of extensions: 28 Number of successful extensions: 8 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: 483 Length adjustment: 33 Effective length of query: 398 Effective length of database: 450 Effective search space: 179100 Effective search space used: 179100 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