Align L-asparaginase; L-ASNase; EC 3.5.1.1; L-asparagine amidohydrolase (uncharacterized)
to candidate WP_086508842.1 BZY95_RS04830 asparaginase
Query= curated2:P30363 (322 letters) >NCBI__GCF_002151265.1:WP_086508842.1 Length = 331 Score = 228 bits (582), Expect = 1e-64 Identities = 131/313 (41%), Positives = 183/313 (58%), Gaps = 6/313 (1%) Query: 4 KVALITTGGTIASRKTESGRLAAGAISGPELAEMCSLPED--VQIDVYPAFQLPSMHITF 61 K+ ++TTGGTIAS+ SGR +GA+ G L SLP D Q++V Q PS ITF Sbjct: 5 KIVVLTTGGTIASQLDASGRNRSGALKGETLLAQVSLPSDFTAQVEVRSLLQKPSNAITF 64 Query: 62 QHLLELKQTIERVFQDGGYDGAVVTHGTDTLEETAYFLDLTIEDERPVVVTGSQRAPEQQ 121 + LL L++ + G V+THGTDTLEETAYFLD+T+ +PVV+TGSQRAP + Sbjct: 65 EDLLGLREACLDIDAQDDVLGIVITHGTDTLEETAYFLDITLPVGKPVVLTGSQRAPHEP 124 Query: 122 GTDAYTNIRHAVYTACSPDIKGAGTVVVFNERIFNARYVKKVHASNLQGFDVFGFGYLGI 181 GTDA+ NI A+ A S G G +VVFN+ IF AR V+KV + GF G LG Sbjct: 125 GTDAFCNIADALKVAASSQAAGLGPLVVFNQSIFAARQVRKVSTFQVHGFAAPDTGPLGY 184 Query: 182 IDNDKVYVYQKLLKRDVH---QLQRPLPAVDIVKCYLDGDGKFIRAAVREGVEGIVLEGV 238 +D +V + + +R ++ +P VDI+ YL I AAV G G+V+EG+ Sbjct: 185 VDGAQVRL-SAIPQRPAGTPLPIESAMPRVDILPAYLGASPSLIEAAVASGAVGLVIEGL 243 Query: 239 GRGQVPPNMMADIEQALNQGVYIVITTSAEEGEVYTTYDYAGSSYDLAKKGVILGKDYDS 298 GRG VPP+ M I +G+ +++ +S G V+ +Y++ GS L GV+ D + Sbjct: 244 GRGHVPPDWMQAIANVTARGIPVMVVSSCASGPVHASYEFIGSLASLESAGVMPVTDLSA 303 Query: 299 KKARMKLAVLLAS 311 +KAR+ L+ LLAS Sbjct: 304 RKARLALSTLLAS 316 Lambda K H 0.318 0.137 0.394 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: 252 Number of extensions: 9 Number of successful extensions: 3 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: 322 Length of database: 331 Length adjustment: 28 Effective length of query: 294 Effective length of database: 303 Effective search space: 89082 Effective search space used: 89082 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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