Align beta-aspartyl-peptidase (EC 3.4.19.5); asparaginase (EC 3.5.1.1) (characterized)
to candidate Echvi_0716 Echvi_0716 Asparaginase
Query= BRENDA::P37595 (321 letters) >FitnessBrowser__Cola:Echvi_0716 Length = 362 Score = 309 bits (792), Expect = 6e-89 Identities = 164/318 (51%), Positives = 214/318 (67%), Gaps = 7/318 (2%) Query: 6 IAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPL 65 + IHGGAG I R MS ++E Y + L+ +E G LEAGE AL V A++++E+ PL Sbjct: 43 LVIHGGAGTIKRENMSEEREKAYRQKLNEALEAGYAQLEAGEPALKAVMAAIKVMEDSPL 102 Query: 66 FNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGE 125 FNAG GAVFT D +E+DA +MDG T AGAVAG++ ++NP+ AA VM SPHV M+G+ Sbjct: 103 FNAGKGAVFTHDGKNEMDAAIMDGKTRNAGAVAGITTVKNPITAAYEVMVNSPHVFMVGK 162 Query: 126 GAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGATVLDHSGA-------PLDEKQKMG 178 GAE FA + +E V PE F RY+QL+ T LDHS P +K G Sbjct: 163 GAEQFAAEQQLEIVDPEYFRDERRYKQLMRIIDAEKTQLDHSSLREMELEDPYFNDRKYG 222 Query: 179 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIR 238 TVGAVA+D DGN+AAATSTGGMTNK GRVGD P++GAG YA+NA+ AVS TG GE FIR Sbjct: 223 TVGAVAVDQDGNIAAATSTGGMTNKRYGRVGDVPVIGAGTYADNATCAVSATGHGEFFIR 282 Query: 239 ALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRA 298 + A++IA++M Y SLA A + VVM++L + GSGG+IAID +GN+A+PFN+ GMYR Sbjct: 283 DVVAHEIASIMRYTDKSLAAAADEVVMKQLVEMEGSGGVIAIDSKGNIAMPFNSAGMYRG 342 Query: 299 WGYAGDTPTTGIYREKGD 316 + P T IY ++ + Sbjct: 343 YIKEKGNPNTFIYDDEDE 360 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: 367 Number of extensions: 25 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: 362 Length adjustment: 28 Effective length of query: 293 Effective length of database: 334 Effective search space: 97862 Effective search space used: 97862 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