Align beta-aspartyl-peptidase (EC 3.4.19.5); asparaginase (EC 3.5.1.1) (characterized)
to candidate CA265_RS15565 CA265_RS15565 beta-aspartyl-peptidase
Query= BRENDA::P37595 (321 letters) >FitnessBrowser__Pedo557:CA265_RS15565 Length = 341 Score = 301 bits (770), Expect = 2e-86 Identities = 162/318 (50%), Positives = 212/318 (66%), Gaps = 9/318 (2%) Query: 3 KAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEE 62 K V+ IHGGAG I + M+ ++E YI L+ ++ G ++AG+S++D V + ++E Sbjct: 25 KYVMVIHGGAGTILKKNMTAEKEAAYIAVLTQALQAGYAEIKAGKSSMDAVEATIHVMEN 84 Query: 63 CPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMM 122 P FNAG GAVFT D +ELDA +MDG TL AG+VAGV+ ++NP+ AAR VME+S HVMM Sbjct: 85 DPHFNAGKGAVFTHDGRNELDAAIMDGKTLMAGSVAGVTTIKNPISAARAVMEKSEHVMM 144 Query: 123 IGEGAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGAT--VLDHSG------APLDEK 174 +G GAE FA G+E V P+ F T R++ L A KE +T VLDH + Sbjct: 145 VGAGAEQFAKEVGLEIVDPKYFWTKERWDGLQKAIKEDSTKAVLDHGNKKSELLGSKNHD 204 Query: 175 QKMGTVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGE 234 K GTVG VALD GNLAA TSTGGMTNK GRVGD+P++GAG Y NN + +SCTG GE Sbjct: 205 YKFGTVGCVALDQAGNLAAGTSTGGMTNKKYGRVGDAPIIGAGTYCNNETAGISCTGWGE 264 Query: 235 VFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEG 294 +IR + A I+ LM+Y GLS+AEA ++ ++K+ +GG GGLIA+D +GNVALPFNTEG Sbjct: 265 FYIRNVVAKTISDLMEYKGLSVAEA-SKIALDKVGKMGGDGGLIALDKKGNVALPFNTEG 323 Query: 295 MYRAWGYAGDTPTTGIYR 312 MYR A IY+ Sbjct: 324 MYRGTITADGKIEVSIYK 341 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: 350 Number of extensions: 18 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: 341 Length adjustment: 28 Effective length of query: 293 Effective length of database: 313 Effective search space: 91709 Effective search space used: 91709 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