Align Isoaspartyl peptidase/L-asparaginase; Asparaginase-like protein 1; Asparaginase-like sperm autoantigen; Beta-aspartyl-peptidase; Glial asparaginase; Isoaspartyl dipeptidase; L-asparagine amidohydrolase; EC 3.4.19.5; EC 3.5.1.1 (characterized)
to candidate N515DRAFT_0391 N515DRAFT_0391 N4-(beta-N-acetylglucosaminyl)-L-asparaginase
Query= SwissProt::Q8VI04 (333 letters) >FitnessBrowser__Dyella79:N515DRAFT_0391 Length = 341 Score = 147 bits (371), Expect = 4e-40 Identities = 112/326 (34%), Positives = 169/326 (51%), Gaps = 34/326 (10%) Query: 20 ASIDVSLVVVVHGGGASNISPGRKELVSE----GIAKAATEGYNILKAGGSAVDAVEGAV 75 A++ + + G A+ +S GRK V G+ A + +L GG A+DAVE V Sbjct: 18 AALSSRIAPALADGKAAGMSGGRKPRVISTWDFGVP-ANLAAWAVLAKGGRALDAVEAGV 76 Query: 76 TMLEND-PEFNAGYGSVLNADGDIEMDASIMDGKDLSAGAVSAVRCIANPVKLARLVMEK 134 + E D + G + DG + +DASIMDG D S GAV+A+ IA+P+++AR VME+ Sbjct: 77 MIPEADLKNHSVGRAGYPDRDGHVSLDASIMDG-DGSCGAVAALEGIAHPIQVARRVMER 135 Query: 135 TPHCFLTGRGAEKFAADMGIPQTPAEKLITERTKK---------------HLEKEKLEKG 179 TPH L G GA++FA + G + EKL+T ++K + E KG Sbjct: 136 TPHVLLVGEGAQQFAVEQGFKK---EKLLTPESEKAWHEWLKTAHYQPSANSEVRDYGKG 192 Query: 180 AQKADCPKNSGTVGAVALDCKGNLAYATSTGGIVNKMVGRVGDSPCIGAGGYADNNLGAV 239 A D N T+G +A+D +G LA A +T G+ K+ GRVGDSP IGAG Y D +G Sbjct: 193 AGGKD---NHDTIGMLAIDAQGRLAGACTTSGMAWKLRGRVGDSPIIGAGLYVDGEVGGA 249 Query: 240 STTGHGESILKVNLARLALFHVEQGKTVDEAATLALDYMKSKLKGLG-----GLILINKT 294 ++TG GE +++ + L + + QG++ +A A+ + K G + IN+ Sbjct: 250 TSTGVGEEVIRNAGSFLVVELMRQGRSPQQACEEAVMRIVKKRPQAAKDLQVGFLAINRE 309 Query: 295 GDWVAKWTSASMPWAAVKNGKLQAGI 320 G+ V + S AV +G Q G+ Sbjct: 310 GE-VGAFAIQSGFSYAVCDGAKQDGL 334 Lambda K H 0.313 0.131 0.379 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: 311 Number of extensions: 15 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: 333 Length of database: 341 Length adjustment: 28 Effective length of query: 305 Effective length of database: 313 Effective search space: 95465 Effective search space used: 95465 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. 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