Align beta-aspartyl-peptidase (EC 3.4.19.5); asparaginase (EC 3.5.1.1) (characterized)
to candidate CCNA_00096 CCNA_00096 L-asparaginase
Query= BRENDA::P37595 (321 letters) >FitnessBrowser__Caulo:CCNA_00096 Length = 292 Score = 211 bits (537), Expect = 2e-59 Identities = 131/294 (44%), Positives = 176/294 (59%), Gaps = 23/294 (7%) Query: 6 IAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPL 65 +A+HGGAGA ++ I + +VE + L AG ALDV E V LE L Sbjct: 8 LALHGGAGAKRGHDYGVE-----IAHMRGLVEAARDRLAAGAGALDVAVETVVGLEASGL 62 Query: 66 FNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGE 125 + AG GA D +ELDA +MDG TL+AG+VA + ++P+LAAR VME +PHVM+ G+ Sbjct: 63 YIAGKGASPNADGEYELDASLMDGATLRAGSVAALQGFKSPILAARAVMEHTPHVMLAGQ 122 Query: 126 GAENFAFARGMERV-SPEIFSTSLRYEQLLAARKEGATVLDHSGAPLDEKQKMGTVGAVA 184 GA FA +G+E V P+ + T + GA +H L GTVG V Sbjct: 123 GAIAFAREQGLETVEDPDAWFT-----------RAGAFEDNHPPDAL----PTGTVGCVV 167 Query: 185 LDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYD 244 D +G LAAATST G+ K PGRVGDSP++GAG +A + AVSCTG GE FIRA A Sbjct: 168 RDGEGRLAAATSTAGVFGKRPGRVGDSPIIGAGAWA-DGHAAVSCTGQGEYFIRAAVAAQ 226 Query: 245 IAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRA 298 IA + +GG +L +A + ++ + ALGG GGLIA+D +GN+A+PF + G+ RA Sbjct: 227 IAHRVRFGGEAL-DAAAQAAIDSVAALGGHGGLIAVDRDGNIAMPFVSSGLKRA 279 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: 317 Number of extensions: 17 Number of successful extensions: 5 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: 292 Length adjustment: 27 Effective length of query: 294 Effective length of database: 265 Effective search space: 77910 Effective search space used: 77910 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