Align beta-aspartyl-peptidase (EC 3.4.19.5); asparaginase (EC 3.5.1.1) (characterized)
to candidate H281DRAFT_04050 H281DRAFT_04050 beta-aspartyl-peptidase (threonine type)
Query= BRENDA::P37595 (321 letters) >FitnessBrowser__Burk376:H281DRAFT_04050 Length = 331 Score = 360 bits (925), Expect = e-104 Identities = 189/327 (57%), Positives = 232/327 (70%), Gaps = 18/327 (5%) Query: 4 AVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEEC 63 AVIAIHGGAG I RA +S E Y AL A++ GQ++L G SALD V+EAVRLLE+C Sbjct: 5 AVIAIHGGAGTILRASLSASAEAEYHAALHAVLAAGQRVLADGGSALDAVSEAVRLLEDC 64 Query: 64 PLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMI 123 PLFNAG GAV+T THELDA +MDG+TL+AGA+ V +RNPVLAAR V+E S HV+ Sbjct: 65 PLFNAGRGAVYTAAGTHELDAAIMDGSTLEAGAICCVKRVRNPVLAARRVLECSEHVLFA 124 Query: 124 GEGAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGATVLDHSGA-------------- 169 GEGAE+FA A+G+E V P+ F T R Q L AR + +LDH GA Sbjct: 125 GEGAESFAAAQGLEFVEPQYFDTEARLRQWLLARDQQRAMLDHDGASLAASPSATDNSDP 184 Query: 170 ----PLDEKQKMGTVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASV 225 P+D +K GTVGAVALD G++AAATSTGG+TNK GRVGD+PL+GAGCYA++A+ Sbjct: 185 VPHEPIDPNRKFGTVGAVALDRHGHVAAATSTGGVTNKQVGRVGDTPLIGAGCYADDATC 244 Query: 226 AVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGN 285 AVS TG+GE+F+R +AAYD+AA M Y +SL EA VVM +LP + G GGLIA+D GN Sbjct: 245 AVSTTGSGEMFMRMVAAYDVAAQMAYRNVSLQEAAHDVVMNRLPKIDGRGGLIAVDALGN 304 Query: 286 VALPFNTEGMYRAWGYAGDTPTTGIYR 312 +ALPFNTEGMYR + G+ PTT IYR Sbjct: 305 IALPFNTEGMYRGFARIGEAPTTAIYR 331 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: 376 Number of extensions: 14 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: 331 Length adjustment: 28 Effective length of query: 293 Effective length of database: 303 Effective search space: 88779 Effective search space used: 88779 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