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 WP_057506804.1 ABB28_RS00800 N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase
Query= SwissProt::Q8VI04 (333 letters) >NCBI__GCF_001431535.1:WP_057506804.1 Length = 334 Score = 136 bits (343), Expect = 6e-37 Identities = 95/251 (37%), Positives = 140/251 (55%), Gaps = 13/251 (5%) Query: 35 ASNISPGRKELVSEGIAKAATE-GYNILKAGGSAVDAVEGAVTMLENDPEFNAGYGSVLN 93 A+ PG + + + A + + L GGSA+DAVE E++ N G N Sbjct: 26 AAAADPGPRVVSTWDFGVGANQVAWKTLADGGSALDAVEQGARWAESEL-CNPTVGRCGN 84 Query: 94 AD--GDIEMDASIMDGKDLSAGAVSAVRCIANPVKLARLVMEKTPHCFLTGRGAEKFAAD 151 D G++ +DASIMDG D G+V+A+ I +PV +AR VMEKTPH L G+GA+ FA + Sbjct: 85 PDRDGNLSLDASIMDG-DGRCGSVAALVDILHPVSVARRVMEKTPHVMLVGQGAQAFAVE 143 Query: 152 MGIPQ----TPAEKLITE---RTKKHLEKEKLEKGAQKADCPKNSGTVGAVALDCKGNLA 204 G P+ TPA + + +T ++ + E+ A D N T+G +A D +G LA Sbjct: 144 QGFPRGKLLTPAAEKAWKAWLKTAEYAPQINAERRAIPGDS-SNHDTLGILARDARGRLA 202 Query: 205 YATSTGGIVNKMVGRVGDSPCIGAGGYADNNLGAVSTTGHGESILKVNLARLALFHVEQG 264 A +T G+ KM GRVGDSP IGAG Y DN +GA + +G GE +++ + L + + QG Sbjct: 203 GACTTSGMAWKMQGRVGDSPIIGAGLYVDNEVGAATASGVGEEMIRNAASFLVVELMRQG 262 Query: 265 KTVDEAATLAL 275 ++ EA A+ Sbjct: 263 RSPAEACREAI 273 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: 289 Number of extensions: 13 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: 334 Length adjustment: 28 Effective length of query: 305 Effective length of database: 306 Effective search space: 93330 Effective search space used: 93330 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 24 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