Align beta-aspartyl-peptidase (EC 3.4.19.5); asparaginase (EC 3.5.1.1) (characterized)
to candidate HSERO_RS09185 HSERO_RS09185 isoaspartyl peptidase
Query= BRENDA::P37595 (321 letters) >FitnessBrowser__HerbieS:HSERO_RS09185 Length = 328 Score = 366 bits (940), Expect = e-106 Identities = 193/320 (60%), Positives = 227/320 (70%), Gaps = 13/320 (4%) Query: 5 VIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECP 64 VIAIHGGAG I+RA ++ + E RY +AL+ IV GQ +L AG SAL+ VTEAVRLLE+CP Sbjct: 5 VIAIHGGAGTITRASLTAEDEARYHQALADIVAAGQAVLNAGGSALEAVTEAVRLLEDCP 64 Query: 65 LFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIG 124 LFNAG GAV+T + HELDACVM+G L +GAVA V++LRNPVLAAR VME S HV+++G Sbjct: 65 LFNAGHGAVYTSEGKHELDACVMNGTDLASGAVACVTNLRNPVLAARTVMEHSEHVLLVG 124 Query: 125 EGAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGATVLDHSGA-------------PL 171 AE+FA G V P F T R+EQ L R + +LDH + P+ Sbjct: 125 PAAESFAARHGAVTVEPGYFHTDARHEQWLRVRGQSRAMLDHDASSFAFAEKAAAPTEPI 184 Query: 172 DEKQKMGTVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTG 231 D K GTVGAVALD GNLAAATSTGG+TNK PGRVGDSP++GAGCYANNA+VAVS TG Sbjct: 185 DPDHKFGTVGAVALDQFGNLAAATSTGGITNKQPGRVGDSPIIGAGCYANNATVAVSATG 244 Query: 232 TGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFN 291 TGE F+R A YDIAA M Y G SL A VV E LP +GG GG+IAID +GN+ALPFN Sbjct: 245 TGEAFMRTAACYDIAARMAYAGQSLEAASHAVVFETLPKVGGRGGVIAIDGQGNLALPFN 304 Query: 292 TEGMYRAWGYAGDTPTTGIY 311 TEGMYRA+G P T IY Sbjct: 305 TEGMYRAYGRGELAPVTAIY 324 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: 383 Number of extensions: 11 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: 328 Length adjustment: 28 Effective length of query: 293 Effective length of database: 300 Effective search space: 87900 Effective search space used: 87900 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