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 CA265_RS08130 CA265_RS08130 glycosylasparaginase
Query= SwissProt::Q8VI04 (333 letters) >FitnessBrowser__Pedo557:CA265_RS08130 Length = 325 Score = 144 bits (362), Expect = 4e-39 Identities = 101/271 (37%), Positives = 148/271 (54%), Gaps = 22/271 (8%) Query: 49 GIAKAATEGYNILKAGGSAVDAVEGAVTMLENDPEFNA-GYGSVLNADGDIEMDASIMDG 107 GIA A + + +L GGSA+DAVE V + E D + GYG + + DG + +DA IMD Sbjct: 30 GIA-ANADAWKVLSTGGSALDAVEQGVWVPEADEHNQSVGYGGLPDRDGHVTLDACIMDE 88 Query: 108 KDLSAGAVSAVRCIANPVKLARLVMEKTPHCFLTGRGAEKFAADMGIPQ----TPA-EKL 162 + GAV A+ I +P+ +AR VMEKTPH L G GA +FA + G + TPA EK Sbjct: 89 LG-NCGAVLALEHIKHPISVARKVMEKTPHVMLAGDGALQFALEQGFKKENLLTPASEKA 147 Query: 163 ITE--RTKKHLEKEKLEKGAQKADCPK-------NSGTVGAVALDCKGNLAYATSTGGIV 213 E +T K+ +E + P+ N T+G +A+D KGN++ A +T G+ Sbjct: 148 WKEWLKTAKYAPVMNIENQLYQKAAPQKLPGNQYNHDTIGMLAIDAKGNISGACTTSGMA 207 Query: 214 NKMVGRVGDSPCIGAGGYADNNLGAVSTTGHGESILKVNLARLALFHVEQGKTVDEAATL 273 K+ GR+GDSP IGAG Y DN +G ++TG GE +++ + L + + QG T + A Sbjct: 208 YKLHGRIGDSPIIGAGLYVDNEVGGATSTGVGEEVVRNVGSFLVVELMRQGYTPEAACKE 267 Query: 274 ALDYMKSKLKGLG-----GLILINKTGDWVA 299 A+ + K G + INK G++ A Sbjct: 268 AVMRIIKKKPETAKNIQVGFLAINKKGEYGA 298 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: 269 Number of extensions: 18 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: 325 Length adjustment: 28 Effective length of query: 305 Effective length of database: 297 Effective search space: 90585 Effective search space used: 90585 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