Align Isoaspartyl peptidase/L-asparaginase; Asparaginase-like protein 1; Beta-aspartyl-peptidase; Isoaspartyl dipeptidase; L-asparagine amidohydrolase; EC 3.4.19.5; EC 3.5.1.1 (characterized)
to candidate 207726 DVU2242 asparaginase family protein
Query= SwissProt::Q8C0M9 (326 letters) >MicrobesOnline__882:207726 Length = 315 Score = 206 bits (523), Expect = 8e-58 Identities = 124/281 (44%), Positives = 168/281 (59%), Gaps = 18/281 (6%) Query: 22 VVVHGGGASNISANRKELVREGIARAATEGYKILKAGGSAVDAVEGAVTVLENDPEFNAG 81 ++VHGG A I A+R+E G RA + +L+ G +AV+AV AV VLE+DP F+AG Sbjct: 6 IIVHGG-AWTIPADRQEAHIAGCRRAVEAAWPLLRDGATAVEAVRAAVNVLEDDPTFDAG 64 Query: 82 YGSVLNVNGDIEMDASIMDGKDLSAGAVSAVRCIANPVKLARLVMEKTPHCFLTGHGAEK 141 G+VLN +G IE+DA+IMDG L G V+AVR ANPV +AR +++ T C L G GAE+ Sbjct: 65 RGAVLNRDGVIELDAAIMDGATLDFGGVAAVRRFANPVDIARRLLD-TEFCLLVGEGAER 123 Query: 142 FAEDMGIPQVPVEKLITERTKKHLEKEKLEKG-------------AQNADCPKNSGTVGA 188 FA + G+ V L+ ER + E + G A D PK GTVGA Sbjct: 124 FALEQGLKPVDPATLLVERERLLYETLRSRAGYSTHDAFRPVTDTAPAGDVPK--GTVGA 181 Query: 189 VALDCRGNLAYATSTGGIVNKMVGRVGDSPCIGAGGYADNNLGAVSTTGHGESILKVNLA 248 VALD GN+A ATSTGG K+ GRVGDSP GAG YADN G S TG GE +++ + Sbjct: 182 VALDIHGNVAAATSTGGTPFKLAGRVGDSPLCGAGTYADNETGGASATGFGEGVMRTLMT 241 Query: 249 RLALFHVEQGKTVEEAAQLALDYMKSKLKGLGGLILVNKTG 289 A H+ + +EAA+ A+D + ++ G GLI++++ G Sbjct: 242 HCACEHLRE-CLPDEAARRAIDMLHRRVGGHAGLIMLDRHG 281 Lambda K H 0.315 0.132 0.384 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: 312 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: 326 Length of database: 315 Length adjustment: 28 Effective length of query: 298 Effective length of database: 287 Effective search space: 85526 Effective search space used: 85526 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 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