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 6937528 Sama_1684 asparaginyl-tRNA synthetase (RefSeq)
Query= curated2:Q8TXG4 (431 letters) >FitnessBrowser__SB2B:6937528 Length = 466 Score = 180 bits (457), Expect = 7e-50 Identities = 138/463 (29%), Positives = 217/463 (46%), Gaps = 49/463 (10%) Query: 2 LKDAYTADVTPERDGEEVRLAGWVHEVRDL-GGIKFVLLRDRTGIVQLTLPKQKVPKETF 60 + + D P G E+ + GWV RD GI F+ + D + + Sbjct: 6 IASVFKGDFAP---GTEITVRGWVRTRRDSKAGISFLAVYDGSCFDAIQGVVPNALSNYN 62 Query: 61 EKVPKLTKESVIRVEGTVQANEKAPGGVEVIPQRIEV---LSESDTHLPLDPTGKVDADL 117 ++V KLT + + G + + + E+ ++V + + DT+ P + Sbjct: 63 DEVLKLTAGCSVEMTGNLVESPGSGQAFELQATAVKVTGWVDDPDTY----PMAAKRHSI 118 Query: 118 DTRLDARVLDLRREEPQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFP 177 + D L R A+ ++RN ++ AI F E GFI V TP I AS EG E+F Sbjct: 119 EHLRDVAHLRPRTNIIGAVARVRNCLSQAIHRFYHENGFIWVSTPIITASDCEGAGEMFR 178 Query: 178 VV--------------------YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEE 217 V +F ++A+L S QL + A ++Y GP FRAE Sbjct: 179 VSTLDMENLPRTDAGKVDYDQDFFGKEAFLTVSGQLNGETY-ACALSKIYTFGPTFRAEN 237 Query: 218 HNTRRHLNEAISVDIEMSFIESEEDVMRVLEELLAHVFRKVREECEKELE---------A 268 NT RHL E V+ E++F + D+ + E +L + F V +E +++ Sbjct: 238 SNTSRHLAEFWMVEPEVAFADLN-DIAGLAESMLKYCFNAVLQERMDDMKFFAERVDGSV 296 Query: 269 LDRELPELETPFERITYEETLDLLSEHG----IEVEWGEDLPTEAERKLGEI-FEEPFFI 323 +DR + + F ++ Y + +++L G VEWG DL +E ER L E F+ P + Sbjct: 297 IDRLQSFVSSDFAQVDYTDAVEILQNCGKTFEYPVEWGIDLQSEHERYLAEEHFKAPVVV 356 Query: 324 TEWPRETRPFYTMAKDDEVTTA-FDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPED 381 +P++ + FY +D T A D++ G+ E+ G+QRE R DVL ++EE LS ED Sbjct: 357 KNYPKDIKAFYMRLNEDGKTVAAMDVLAPGIGEIIGGSQREERLDVLDARLEEMNLSKED 416 Query: 382 FRHYLEAFKYGMPPHGGWGLGLERTLMTITGAENIREVTLFPR 424 + Y + +YG PH G+GLG ER + +TG NIR+V FPR Sbjct: 417 YWWYRDLRRYGTVPHAGFGLGFERLVSYVTGVGNIRDVIPFPR 459 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: 457 Number of extensions: 23 Number of successful extensions: 4 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: 466 Length adjustment: 33 Effective length of query: 398 Effective length of database: 433 Effective search space: 172334 Effective search space used: 172334 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