Align asparagine-tRNA ligase (EC 6.1.1.22); aspartate-ammonia ligase (EC 6.3.1.1) (characterized)
to candidate WP_084516684.1 H567_RS0100320 asparagine--tRNA ligase
Query= BRENDA::Q9V228 (294 letters) >NCBI__GCF_000422285.1:WP_084516684.1 Length = 474 Score = 79.3 bits (194), Expect = 2e-19 Identities = 83/316 (26%), Positives = 138/316 (43%), Gaps = 59/316 (18%) Query: 28 FFTDRGFKWL-LPIMLSP-----------ITDPLWPDPAGEGIRPAEVDVYGVRMRLTHS 75 FF +RGF ++ PI+ T L P EG D +G LT S Sbjct: 160 FFQERGFLYVHTPIITGSDCEGAGDLFHITTFDLGAVPIEEGRVDFSEDFFGQPANLTVS 219 Query: 76 MILHKQLAIAMGLEKIFVLSPNIRLESRRKDDGRHSYEFTQLDFEIEGAKMKDVMRLIEE 135 L ++ A+ L ++ P R E+ + RH EF ++ E+ +++ M L E Sbjct: 220 GQLEAEI-YALALGDVYTFGPTFRAEN--SNTSRHLAEFWMVEPEMAFCELEGDMDLAVE 276 Query: 136 LIYGLFRKAE-------EWTGR----------EFPRARHFKVYDYKDILE---------- 168 + LFR E+ R E + F+ Y + +E Sbjct: 277 FLQYLFRHVLDHCRGDLEFFNRFIDQSVIGTLETLATQDFERLSYTEAIEILSKSGEEFE 336 Query: 169 ---EFGSDEKASME-------MEEPFWIVNIPRE---FYDR--EENGVWKNYDLILPYGY 213 +G+D ++ E ++P + + P+ FY + + + D+++P Sbjct: 337 FPVAWGTDLQSEHERYLCEKTFKKPVILTDYPKTIKPFYMKLNPDGKTVRAMDVLVPK-I 395 Query: 214 GEVSSGGEREWEYEKIVAKIRAAGLKEDSFRPYLEIARAGKLKPSAGAGIGVERLVRFIV 273 GE+ G +RE +Y+ ++ +I +GL D + YL++ R G P AG G+G+ERLV+FI Sbjct: 396 GEIIGGSQREDDYDTLLQRIEESGLHVDDYWWYLDLRRFGST-PHAGFGLGLERLVQFIT 454 Query: 274 GAKHIAEVQPFPRVPG 289 G +I +V PFPR PG Sbjct: 455 GMGNIRDVIPFPRTPG 470 Lambda K H 0.322 0.142 0.428 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: 350 Number of extensions: 18 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 294 Length of database: 474 Length adjustment: 30 Effective length of query: 264 Effective length of database: 444 Effective search space: 117216 Effective search space used: 117216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 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