Align beta-aspartyl-peptidase (EC 3.4.19.5); asparaginase (EC 3.5.1.1) (characterized)
to candidate WP_057687409.1 ABB28_RS16220 isoaspartyl peptidase/L-asparaginase
Query= BRENDA::P37595 (321 letters) >NCBI__GCF_001431535.1:WP_057687409.1 Length = 342 Score = 276 bits (705), Expect = 7e-79 Identities = 153/310 (49%), Positives = 200/310 (64%), Gaps = 4/310 (1%) Query: 5 VIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECP 64 ++ IHGGAG + RA +S ++E EAL + + G L+AG AL VT A+ +LE+ P Sbjct: 30 LLVIHGGAG-VQRAGLSAEEERAAREALRSALLQGHAELKAGRPALAAVTRAITVLEDDP 88 Query: 65 LFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIG 124 FNAG GAVFT D +ELDA +M+G T +AGAVAGV +RNP+L A+ VM S HVMM+G Sbjct: 89 TFNAGRGAVFTHDGRNELDAALMEGATRRAGAVAGVQRVRNPILLAQAVMAHSAHVMMVG 148 Query: 125 EGAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGATVLDHSGAPLDEKQKMGTVGAVA 184 +GAE FA +G+ V P F T R++QL A +E H A L+ + GTVGA+A Sbjct: 149 QGAEAFAAEQGVALVDPSYFRTEKRWQQLQRALQEERAGQAH--AELETARHFGTVGALA 206 Query: 185 LDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYD 244 LD G LAA TSTGGMTNK GRVGDSP++GAG +A+ AVS TG GE ++R AA++ Sbjct: 207 LDAAGTLAAGTSTGGMTNKRYGRVGDSPIIGAGTWADE-GCAVSGTGWGEYYLRTAAAHE 265 Query: 245 IAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGD 304 I A + G S A+A V+ E +PALGG GG I + +G + LPFNTEGMYR W A Sbjct: 266 ICARVRLAGASAAQAGREVINEMIPALGGDGGAIVLTAKGEIGLPFNTEGMYRGWIGADG 325 Query: 305 TPTTGIYREK 314 P I+ ++ Sbjct: 326 VPHVAIFADE 335 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: 337 Number of extensions: 17 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: 321 Length of database: 342 Length adjustment: 28 Effective length of query: 293 Effective length of database: 314 Effective search space: 92002 Effective search space used: 92002 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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