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 N515DRAFT_3733 N515DRAFT_3733 asparaginyl-tRNA synthetase
Query= curated2:Q8TXG4 (431 letters) >FitnessBrowser__Dyella79:N515DRAFT_3733 Length = 466 Score = 170 bits (431), Expect = 7e-47 Identities = 138/451 (30%), Positives = 214/451 (47%), Gaps = 50/451 (11%) Query: 16 GEEVRLAGWVHEVRDL-GGIKFVLLRDRTGI--VQLTLPKQKVPKETFEKVPKLTKESVI 72 G + + GWV RD G+ FV + D + +Q +P ET +V LT + + Sbjct: 17 GSKATVRGWVRTRRDSKAGLSFVNITDGSCFAPIQAVVPATLANYET--EVKHLTAGAGL 74 Query: 73 RVEGTVQANEKAPGGVEVIPQRIEV---LSESDTHLPLDPTGKVDADLDTRLDARVLDLR 129 V GT+ ++ E+ + ++V + + +T+ P+ P ++ + L R Sbjct: 75 IVSGTLVPSQGQGQAFELQAESVQVTGFVDDPETY-PIQPK---QHSMEFLREVAHLRPR 130 Query: 130 REEPQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV---------- 179 A+ ++R+ + TAI L E+GF ++TP I S EG ++F + Sbjct: 131 TNLFGAVTRVRHTMMTAIHRHLTEQGFFWINTPIITTSDAEGAGDMFRLSTLDLANLPRT 190 Query: 180 ----------YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAIS 229 +F R+A+L S QL + A +VY GP FRAE NT RHL E Sbjct: 191 PDGKIDFRKDFFGREAFLTVSGQLNVEAY-ALAMSKVYTFGPTFRAENSNTPRHLAEFWM 249 Query: 230 VDIEMSFIESEEDVMRVLEELLAHVFRKVREECEKELEAL-DRELPELET--------PF 280 V+ E++F + D E L +F+ V +E ++ +R LP+ T PF Sbjct: 250 VEPEIAFADLAADA-DCAEAFLKAIFKAVLDERADDMAFFAERVLPDAITRLENFIAQPF 308 Query: 281 ERITYEETLDLLSEHGIEVE----WGEDLPTEAERKLGEIFE-EPFFITEWPRETRPFYT 335 ERI Y E +++L G + E WG DL TE ER L E P + +P + + FY Sbjct: 309 ERIDYTEAVEILKNCGQKFEFPVAWGIDLQTEHERYLAEKHVGRPVVVMNYPEQIKAFYM 368 Query: 336 MAKDDEVTTA-FDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAFKYGM 393 DDE T A D++ G+ E+ G+QRE R D L R++ + GL + Y + +YG Sbjct: 369 RLNDDEKTVAAMDVLAPGIGEIIGGSQREERLDYLDRRMAKFGLDAATYGWYRDLRRYGT 428 Query: 394 PPHGGWGLGLERTLMTITGAENIREVTLFPR 424 PH G+GLG ER L+ + G NIR+ +PR Sbjct: 429 VPHAGFGLGFERLLVYVCGLANIRDAIPYPR 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: 473 Number of extensions: 31 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: 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