Align beta-aspartyl-peptidase (EC 3.4.19.5); asparaginase (EC 3.5.1.1) (characterized)
to candidate N515DRAFT_1733 N515DRAFT_1733 beta-aspartyl-peptidase (threonine type)
Query= BRENDA::P37595 (321 letters) >FitnessBrowser__Dyella79:N515DRAFT_1733 Length = 329 Score = 288 bits (737), Expect = 1e-82 Identities = 158/312 (50%), Positives = 204/312 (65%), Gaps = 4/312 (1%) Query: 5 VIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECP 64 V+ IHGGAG I M+ +E AL+ ++ G L+AG+ A+D VT A+ +LE P Sbjct: 8 VLVIHGGAGVIKH-DMNPAREKAVRAALTQALQNGYAQLKAGKPAMDAVTAAITVLENDP 66 Query: 65 LFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIG 124 FNAG GAVFT D +ELDA VMDG TLKAGA+AGV ++NP+L AR VME+S HVM+ G Sbjct: 67 NFNAGKGAVFTHDGKNELDAAVMDGYTLKAGAIAGVHRVKNPILLARAVMEKSQHVMLAG 126 Query: 125 EGAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGATVLDHSGAPLDEKQKMGTVGAVA 184 +GAE FA G+E V P F T R++QL A KE A H ++ + GTVGAVA Sbjct: 127 DGAEAFAKEAGIELVDPAYFRTEERWQQLQKALKEDAEHRQHE--DVETAKHFGTVGAVA 184 Query: 185 LDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYD 244 LD G LAA TSTGGMTNK GR+GDSPL+GAG YANN AVS TG GE +IR +AA++ Sbjct: 185 LDAQGRLAAGTSTGGMTNKRWGRIGDSPLIGAGTYANN-GCAVSGTGWGEFYIRTVAAHE 243 Query: 245 IAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGD 304 I + + L A V+ +++P++GG+GG IA+D +GNVA+PFNT+GM+R W Sbjct: 244 ICMRVTQMRVPLKRAAAEVINQEIPSMGGNGGAIALDAQGNVAMPFNTDGMFRGWIAEDG 303 Query: 305 TPTTGIYREKGD 316 P IY + D Sbjct: 304 KPHVAIYGDDDD 315 Lambda K H 0.316 0.133 0.377 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: 348 Number of extensions: 21 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: 321 Length of database: 329 Length adjustment: 28 Effective length of query: 293 Effective length of database: 301 Effective search space: 88193 Effective search space used: 88193 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: 41 (21.6 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