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 Echvi_4056 Echvi_4056 Asparaginase
Query= SwissProt::Q8C0M9 (326 letters) >FitnessBrowser__Cola:Echvi_4056 Length = 327 Score = 161 bits (408), Expect = 2e-44 Identities = 102/249 (40%), Positives = 145/249 (58%), Gaps = 8/249 (3%) Query: 47 AATEGYKILKAGGSAVDAVEGAVTVLEND-PEFNAGYGSVLNVNGDIEMDASIMDGKDLS 105 A + +++L+ G+ VDAVE V V END + G + + G + +DASIM G D S Sbjct: 53 ANDKAWEVLEKSGNIVDAVEQGVMVTENDLKNLSVGLQGLPDREGIVTLDASIMKG-DGS 111 Query: 106 AGAVSAVRCIANPVKLARLVMEKTPHCFLTGHGAEKFAEDMGIPQVPVEKLITERTKKHL 165 G+V VR + +P+ LAR VME TPH L G GA +FA G P E ++ +K Sbjct: 112 CGSVCFVRQVKHPISLARKVMEDTPHVMLAGEGARQFAIQEGFPIEKEE--LSPAAEKAY 169 Query: 166 EKEKLEKGAQNADCPKNSGTVGAVALDCRGNLAYATSTGGIVNKMVGRVGDSPCIGAGGY 225 EK KL+ + +N T+G + LD GNLA + +T G+ KM GRVGDSP IGAG Y Sbjct: 170 EKWKLKSEYKPVINIENHDTIGMIGLDQNGNLAGSCTTSGLAYKMHGRVGDSPIIGAGLY 229 Query: 226 ADNNLGAVSTTGHGESILKVNLARLALFHVEQGKTVEEAAQLALDYMKSKLKGL----GG 281 DN +GA + TG GESI+K+ + L + + QG++ +EA + A+ + SK KG+ G Sbjct: 230 VDNEVGAATATGLGESIIKICGSFLIVELMRQGRSPQEACEEAVRRLISKNKGIEGIQAG 289 Query: 282 LILVNKTGD 290 + VNK G+ Sbjct: 290 FLAVNKDGE 298 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: 263 Number of extensions: 11 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: 326 Length of database: 327 Length adjustment: 28 Effective length of query: 298 Effective length of database: 299 Effective search space: 89102 Effective search space used: 89102 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