Align beta-aspartyl-peptidase (EC 3.4.19.5); asparaginase (EC 3.5.1.1) (characterized)
to candidate 201272 SO2115 asparaginase family protein (NCBI ptt file)
Query= BRENDA::P37595 (321 letters) >FitnessBrowser__MR1:201272 Length = 326 Score = 286 bits (731), Expect = 6e-82 Identities = 155/313 (49%), Positives = 203/313 (64%), Gaps = 4/313 (1%) Query: 6 IAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPL 65 IAIHGGAG IS+A ++ + Y + L V+ G K+LE G +L V A+ +LE PL Sbjct: 14 IAIHGGAGTISKANLTPELRQAYKDKLKEAVDKGSKVLEQGGDSLVAVQTAINVLENSPL 73 Query: 66 FNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGE 125 FNAG+G+V+T D HELDA +MDG T+ AGAVAGV H+ NP+ A VM +S HVM+ G Sbjct: 74 FNAGVGSVYTYDGGHELDASIMDGKTMNAGAVAGVRHIANPIDLALAVMNKSEHVMLSGA 133 Query: 126 GAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGATVLDH---SGAPLDEKQ-KMGTVG 181 GAE FA +G V+ F + RY+QLL AR++ +G +++ K GTVG Sbjct: 134 GAEEFALTQGFTLVANSHFDSDARYQQLLDARQKLQAAQKSEQIAGIEMNDLDYKFGTVG 193 Query: 182 AVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALA 241 AVALD +GNLAA TSTGGMT K GR+GDSP++GAG YA N AVS TG GE FIR Sbjct: 194 AVALDKNGNLAAGTSTGGMTAKRFGRIGDSPVIGAGTYAENGVCAVSATGHGEFFIRYQV 253 Query: 242 AYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGY 301 A DI A + Y S+ +A + V+ ++L GGSGG+IA+DH GN+A PFNTEGMYRA Sbjct: 254 AGDICARVKYQQKSILQAADEVINQRLITAGGSGGVIAVDHRGNIATPFNTEGMYRASRS 313 Query: 302 AGDTPTTGIYREK 314 G+ I++++ Sbjct: 314 NGEPAQVMIWQDQ 326 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: 341 Number of extensions: 16 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: 326 Length adjustment: 28 Effective length of query: 293 Effective length of database: 298 Effective search space: 87314 Effective search space used: 87314 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