Align beta-aspartyl-peptidase (EC 3.4.19.5); asparaginase (EC 3.5.1.1) (characterized)
to candidate BPHYT_RS15545 BPHYT_RS15545 isoaspartyl peptidase
Query= BRENDA::P37595 (321 letters) >FitnessBrowser__BFirm:BPHYT_RS15545 Length = 330 Score = 362 bits (929), Expect = e-105 Identities = 188/326 (57%), Positives = 231/326 (70%), Gaps = 17/326 (5%) Query: 4 AVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEEC 63 AVIAIHGGAG I R MS E Y AL A++ GQ++L G SALD V+EAVRLLE+C Sbjct: 5 AVIAIHGGAGTILRTSMSASAEAEYHAALHAVLSAGQRVLTDGGSALDAVSEAVRLLEDC 64 Query: 64 PLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMI 123 PLFNAG GAV+T THELDA +MDG+TL+AGA+ V +RNP+LAAR V+E+S HV+ Sbjct: 65 PLFNAGRGAVYTAAGTHELDAAIMDGSTLEAGAICCVKRVRNPILAARRVLERSEHVLFT 124 Query: 124 GEGAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGATVLDHSGA-------------- 169 GEGAE FA A+G+E PE F T R+ Q L AR + +LDH GA Sbjct: 125 GEGAEAFAAAQGLEFAEPEYFHTEARHRQWLIARGQQRAMLDHDGATLAAAPSPNDGDPT 184 Query: 170 ---PLDEKQKMGTVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVA 226 P+D +K GTVGAVALD G++AAATSTGG+TNK GRVGD+PL+GAGCYA++A+ A Sbjct: 185 PHEPIDPNRKFGTVGAVALDQHGHVAAATSTGGVTNKQAGRVGDTPLIGAGCYADDATCA 244 Query: 227 VSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNV 286 VS TG+GE+F+R +AAYD+AA M Y +SL EA + VVM +LP + G GGLIA+D GNV Sbjct: 245 VSTTGSGEMFMRMVAAYDVAAQMAYRNVSLQEAADDVVMNRLPKIDGRGGLIAVDARGNV 304 Query: 287 ALPFNTEGMYRAWGYAGDTPTTGIYR 312 LPFNTEGMYR + G+TP T IYR Sbjct: 305 TLPFNTEGMYRGFARLGETPVTAIYR 330 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: 375 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: 330 Length adjustment: 28 Effective length of query: 293 Effective length of database: 302 Effective search space: 88486 Effective search space used: 88486 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