Align beta-aspartyl-peptidase (EC 3.4.19.5); asparaginase (EC 3.5.1.1) (characterized)
to candidate 5209718 Shew_2171 peptidase T2, asparaginase 2 (RefSeq)
Query= BRENDA::P37595 (321 letters) >FitnessBrowser__PV4:5209718 Length = 348 Score = 298 bits (763), Expect = 1e-85 Identities = 162/317 (51%), Positives = 206/317 (64%), Gaps = 9/317 (2%) Query: 6 IAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPL 65 IAIHGGAG IS+A ++ Q+ Y + L V+ G K+LE G +L VT A+ +LE+ PL Sbjct: 31 IAIHGGAGTISKANLTEAQQQAYRDKLKEAVDAGYKVLEKGGDSLTAVTTAINILEDSPL 90 Query: 66 FNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGE 125 FNAG GAV+T D THE+DA +MDG L AGAVAGV H++NP+ AR VM++SPHVM+ G+ Sbjct: 91 FNAGKGAVYTYDGTHEMDASIMDGRNLNAGAVAGVKHIKNPINLARAVMDKSPHVMLSGQ 150 Query: 126 GAENFAFARGMERVSPEIFSTSLRYEQLLAAR-KEGATVLDHSGAP--------LDEKQK 176 GAE FA ++ V F T RY+QL+ A+ K A +G P LD K Sbjct: 151 GAEEFALSQDFSLVPVTYFDTESRYQQLIDAKAKLKAAESKEAGKPDYQASVNYLDLDYK 210 Query: 177 MGTVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVF 236 GTVGAVALD GNLAA TSTGGMT K GR+GDSP++GAG YA N AVS TG GE F Sbjct: 211 FGTVGAVALDKQGNLAAGTSTGGMTVKRFGRIGDSPVIGAGTYAENQVCAVSATGHGEYF 270 Query: 237 IRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMY 296 IR A DI A + Y S+ +A + V+ ++L GG+GG+IAID GN+A PFNTEGMY Sbjct: 271 IRYHVAGDICAKVKYQQKSILQAADEVINQRLITAGGTGGVIAIDQRGNIATPFNTEGMY 330 Query: 297 RAWGYAGDTPTTGIYRE 313 RA G+ I+++ Sbjct: 331 RATRKGGEPAKVMIWQD 347 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: 360 Number of extensions: 16 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: 348 Length adjustment: 28 Effective length of query: 293 Effective length of database: 320 Effective search space: 93760 Effective search space used: 93760 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 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